Sequence
atgc intronic sequence ATGC exonic sequencegttggttgaattgtctgcacatcattacacacgcgtgttcggacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgcatgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGTGATCTT
Basic information
species | Glycine max |
transcript | GLYMA01G36870.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------gttggttgaattgtctgcacatcatt----acacacgcgtgttcggacat--gcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgcatgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGTGATCTT
| | ||| | || | ||||| | || || || | | | ||| || | || | ||||| |||||||| ||| |||||||||||| ||| ||| |||||||| || || ||| | ||| |||||||||| |||| || |||||||||||||||||||||| ||||| || || ||||||| |||||| || || ||| ||||| | ||||| |||
gtgagttatgatttaagattgttatacacccttctactcattttggaaacgagcttgccagaatgtttgcacttcatggagatttaattggactatgagagcatgatt-ctgatcatgcaggtgttgtattgcttgtgaatcatt---accctttgatgatcctgagttgaagcttcctatcgggctttctggtctgcagGGACCTGCTCGAGAAAAGGAGAGACGGGAGAAAGAGAGGGGCGAGCTTCGTGACCTT
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 5
gttggttgaattgtctgcacatcattacacacgcgtgttcggacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgca--tgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGTGATCTT
||||||| ||||||||||||||| || ||| |||||||| ||||||||||||||||| ||||||||||||||||| |||| ||||||||||||||||| ||||| ||||| ||||||||||||||||| ||| |||||||| | ||||||||
--------------------------------------------------------------------------------atgatttgtggtcatgcaggtgttatagtgctcttgtgaatcattcatactcttagctgatcctgagttgaggcttgcaatcggcctttctggtctgcagGGACCTGCACGGGAAAAGGAGAAACGGGAAAAAGAACGGAGCGAGCTTCGTGATCTC
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S456_14V6.1 (Physcomitrella patens), 3'ss of exon 5
gttggttgaattgtctgcacatcattacacacgcgtgtt-cggacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtag-taatgcatgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGTGATCTT
|| ||| || | | | ||| | || | | | | |||||| | || || ||| | | | | | | | || ||| || | | || || ||| | | | | | |||| | |||| ||||| |||||||||||||| |||||||||||| | || || | |||||| |
------------------------gtaagcacaattgatactcatatgtacgttgcgatga-gataaaacatcactatt-cagtatgcttggactcgttgcagaaaattctagttgggaacgttctccaattttttcttacctcgcttcctaatgggattgcattctttgtcccaccaagGGTCCTGCTCGGGAGAAGGAGAAGCGGGAAAAGGAACGAAGTGAACTTCGTGATTTG
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S313_104V6.1 (Physcomitrella patens), 3'ss of exon 5
gttggttgaattgtctgcacatcattacacacgcgtgttcggacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgcatgtgaatctttcatactcttagctgaccctga-gttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGTGATCTT
| || ||| || || || | || | || | || | | || || | | || | ||| | | | || || || | ||||| ||||| ||||||||||||||||| ||||||||| |||||||||||||||| |
---------------------------------------------------------------------gtttggaaagcagcatcg------gtgtagagttcgtca---atcgagacgttgtggattatttgcgcatgccgaagctgacgttggttgatcatattgatg-taaacagGGCCCTGCTCGGGAGAAGGAGAAACGAGAAAAGGAACGGAGCGAGTTGCGTGACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGTGATCTT
agctgac putative branch site (score: 3)
ctttct putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggttgaattgtctgcacatcattacacacgcgtgttcggacatgcatgtcgtcacaatagttgcacatcatgagggcatgatttctggtcatgcaggtgtagtaatgcatgtgaatctttcatactcttagctgaccctgagttgaggcttgctgtcgggctttctggtctgcagGGGCCTGCCCGGGAGAAGGAGAAACGGGAAAAGGAAAGGAGCGAGTTGCGTGATCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG