Sequence
atgc intronic sequence ATGC exonic sequencegtaaacttctcatcttgccgatgcttattttcttaaaatataacaataatttgtgcttgctccactccagATGGTCTGCCATCACCTCGATAGAAATATCCCAGAAGATGTAGCATTTGCCGAGTCTAGAATTCGAGCTGAAACAATAGCTGCTGAGGATATCTTGCATG
Basic information
species | Oryza sativa |
transcript | 13114.m00153 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 13
----gtaaacttctcatcttgc-cgatgcttattttcttaaaatataacaataatttgtgcttgctccactccagATGGTCTGCCATCACCTCGATAGAAATATCCCAGAAGATGTAGCATTTGCCGAGTCTAGAATTCGAGCTGAAACAATAGCTGCTGAGGATATCTTGCATG
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gtatgcaattatccaattcagcactgtagatacagtgtacaattttcatggtaatatgttgtgattatagtgcagATGGTTTGTCACCACCTTGATAAAAACATTCCAGAAGATGTAGCATTTGCCGAGTCTAGAATTCGAGCTGAAACAATTGCTGCTGAGGACATATTGCATG
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 14
------gtaaacttctcatcttgccgatgcttattttcttaaaatataacaataatttgtgcttgctccac-tccagATGGTCTGCCATCACCTCGATAGAAATATCCCAGAAGATGTAGCATTTGCCGAGTCTAGAATTCGAGCTGAAACAATAGCTGCTGAGGATATCTTGCATG
|| | | | || | || | | | ||||||| ||| | | | ||||||||||||||||| || ||| ||||| |||||||||||||| ||||| || || ||||| ||||||||||||| |||||||| ||||| || ||||
gtatgcaacaaatcacaaaagtaatagtgtacagcttgtgctatttggctcttaatttgcgctcgtatgatgtacagATGGTCTGCCATCATCTTAATAAGAATATTCCAGAAGATGTAGCTTTTGCTGAATCAAGAATAAGAGCTGAAACAATTGCTGCTGAAGATATTTTACATG
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 16
lower sequence: AT1G67550.1 (Arabidopsis thaliana), 3'ss of exon 13
--gtaaacttctcatcttgccgatgcttattttcttaaaatataac-----aataattt-gtgcttgctccactccagATGGTCTGCCATCACCTCGATAGAAATATCCCAGAAGATGTAGCATTTGCCGAGTCTAGAATTCGAGCTGAAACAATAGCTGCTGAGGATATCTTGCATG
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gtatgagaattttatacgagtgatggtgaattgctttacttttgtcttgttaataacctcatatgcaaacacaaacagATGGTTTGCCATCACCTTGACAAGAACATCCCAGAAGATGTAGCTTTTGCTGAATCAAGAATAAGAGCTGAAACAATAGCTGCAGAGGATATATTGCATG
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 13
--gtaaacttctcatcttgccg-atgcttattttcttaaaatataaca-ataatttgtgcttgctccactccagATGGTCTGCCATCACCTCGATAGAAATATCCCAGAAGATGTAGCATTTGCCGAGTCTAGAATTCGAGCTGAAACAATAGCTGCTGAGGATATCTTGCATG
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gtatgaaaagattatgaagatatatggtaactttttggacagttgacttgtaaattgatctgattaca-tgcagATGGTCTGCCATCACCTTGATAAGGATATTCCAGAAGATGTAGCCTTTGCTGAATCACGAATAAGAGCTGAAACAATTGCTGCTGAAGACATTTTGCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccgatgcttattttcttaaaatataacaataatttgtgcttgctccactccagATGGTCTGCCATCACCTCGATAGAAATATCCCAGAAGATGTAGCATTTGCCGAGTCTAGAATTCGAGCTGAAACAATAGCTGCTGAGGATATCTTGCATG
atataac putative branch site (score: 3)
ctccactcc putative PPT
atgcttattttcttaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacttctcatcttgccgatgcttattttcttaaaatataacaataatttgtgcttgctccactccagATGGTCTGCCATCACCTCGATAGAAATATCCCAGAAGATGTAGCATTTGCCGAGTCTAGAATTCGAGCTGAAACAATAGCTGCTGAGGATATCTTGCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT