Stem-loop sequence cin-mir-4001a-1

Accession

MI0015510

Description

Ciona intestinalis miR-4001a-1 stem-loop

Stem-loop

ug       ua    ca     cuu 
  gaacuua  cgaa  ggcug   u
  |||||||  ||||  |||||   g
  uuugaau  gcuu  cuggc   u
-a       uc    ca     uca 

Genome context

Coordinates (JGI2)	Overlapping transcripts
7q: 5401442-5401493 [-]	antisense ENSCINT00000015751 ; F6SJL3_CIOIN; intron 20 ENSCINT00000015751 ; F6SJL3_CIOIN; intron 20 ENSCINT00000015772 ; F6SIN5_CIOIN; intron 21 ENSCINT00000015772 ; F6SIN5_CIOIN; intron 21 ENSCINT00000015751 ; F6SJL3_CIOIN; intron 21 ENSCINT00000015758 ; F6SJH3_CIOIN; intron 22 ENSCINT00000015758 ; F6SJH3_CIOIN; intron 22 ENSCINT00000015772 ; F6SIN5_CIOIN; intron 22 ENSCINT00000015758 ; F6SJH3_CIOIN; intron 23
7q: 5402621-5402672 [-]	antisense ENSCINT00000015751 ; F6SJL3_CIOIN; intron 20 ENSCINT00000015751 ; F6SJL3_CIOIN; intron 20 ENSCINT00000015772 ; F6SIN5_CIOIN; intron 21 ENSCINT00000015772 ; F6SIN5_CIOIN; intron 21 ENSCINT00000015751 ; F6SJL3_CIOIN; intron 21 ENSCINT00000015758 ; F6SJH3_CIOIN; intron 22 ENSCINT00000015758 ; F6SJH3_CIOIN; intron 22 ENSCINT00000015772 ; F6SIN5_CIOIN; intron 22 ENSCINT00000015758 ; F6SJH3_CIOIN; intron 23
7q: 5411814-5411865 [-]	antisense ENSCINT00000015751 ; F6SJL3_CIOIN; intron 20 ENSCINT00000015751 ; F6SJL3_CIOIN; intron 20 ENSCINT00000015772 ; F6SIN5_CIOIN; intron 21 ENSCINT00000015772 ; F6SIN5_CIOIN; intron 21 ENSCINT00000015751 ; F6SJL3_CIOIN; intron 21 ENSCINT00000015758 ; F6SJH3_CIOIN; intron 22 ENSCINT00000015758 ; F6SJH3_CIOIN; intron 22 ENSCINT00000015772 ; F6SIN5_CIOIN; intron 22 ENSCINT00000015758 ; F6SJH3_CIOIN; intron 23

Clustered miRNAs

< 10kb from cin-mir-4001a-1

• cin-mir-4006b: 7q: 5412601-5412650 [-]
• cin-mir-4006e: 7q: 5412237-5412283 [-]
• cin-mir-4001a-1: 7q: 5411814-5411865 [-]
• cin-mir-4001a-2: 7q: 5411381-5411431 [-]
• cin-mir-4002: 7q: 5411380-5411432 [+]
• cin-mir-4001h: 7q: 5411022-5411071 [-]
• cin-mir-4000a-2: 7q: 5410807-5410861 [-]
• cin-mir-4006a-2: 7q: 5410620-5410672 [-]
• cin-mir-4006a-3: 7q: 5410518-5410568 [-]
• cin-mir-4006a-1: 7q: 5410360-5410408 [-]
• cin-mir-4006e: 7q: 5403043-5403089 [-]
• cin-mir-4001a-1: 7q: 5402621-5402672 [-]
• cin-mir-4006b: 7q: 5402317-5402366 [-]
• cin-mir-4000c: 7q: 5402053-5402104 [-]
• cin-mir-4006e: 7q: 5401862-5401908 [-]
• cin-mir-4000b-2: 7q: 5401574-5401625 [-]
• cin-mir-4001a-1: 7q: 5401442-5401493 [-]
• cin-mir-4000b-1: 7q: 5401203-5401256 [-]
• cin-mir-4001a-2: 7q: 5401049-5401099 [-]
• cin-mir-4002: 7q: 5401048-5401100 [+]
• cin-mir-4000d: 7q: 5400845-5400896 [-]
• cin-mir-4001h: 7q: 5400692-5400741 [-]
• cin-mir-4006a-3: 7q: 5400214-5400264 [-]
• cin-mir-4006a-1: 7q: 5400066-5400114 [-]
• cin-mir-4000a-1: 7q: 5398797-5398851 [-]

Database links

• ENTREZGENE: 100498876;mir4001a-1

Mature sequence cin-miR-4001a-5p

• Accession: MIMAT0016444
• Sequence: 1 - uggaacuuauacgaacaggc - 20
• Evidence: experimental; Solexa [1]

Mature sequence cin-miR-4001a-1-3p

• Accession: MIMAT0016445
• Sequence: 34 - gucacuucgcuuaaguuua - 52
• Evidence: experimental; Solexa [1]

References

1. PMID:20370911 "miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data" Hendrix D, Levine M, Shi W Genome Biol. 11:R39(2010).