Sequence
atgc intronic sequence ATGC exonic sequencegtaagtattatataagttaataatgcatgcaacaagtacatattcattaaccgataaaaaaaagtcatccattaattaataaactaatcaattttgtcattactttttagATACTCAATCCCACAGAATTTTTAGGGAACATTGTGGTTGAACATGATTATGCTGAGTGCACTGGATCTGCTATTCAAGCTTTAGTTTTGTTTAAGAAGC
Basic information
species | Glycine max |
transcript | GLYMA03G27660.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G27660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtattatataagttaataatgcatgcaacaagtacatattcattaaccgataaaaaaaagtcatccattaattaataaactaatcaattttgtcattactttttagATACTCAATCCCACAGAATTTTTAGGGAACATTGTGGTTGAACATGATTATGCTGAGTGCACTGGATCTGCTATTCAAGCTTTAGTTTTGTTTAAGAAGC
|||| | | | | ||| | | ||| |||| | | | ||| | | | ||| | || | || || || ||| ||| || || ||| | | | ||| || | |||| | || ||| ||| | | | | | ||| | | |
-----------gtaagattcttgataacagaccaactttcttttc--taactttgatagctttaacgtccttgga--gactaacagaacagtgatgcagGTATGTTGAGTGCACTGCATCAGCCA-----TTCAGGCTCTAGTTTTGTTTAAGA-AGTTATACCCAGGACACAGGAAGAACGAGATAGAC---AATTTCATCACAAAT--
upper sequence: GLYMA03G27660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01280.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtattatataagttaataatgcatgcaacaagtacatattcattaaccgataaaaaaaagtcatccattaattaataaactaatcaattttgtcattactttttagATACTCAATCCCACAGAATTTTTAGGGAACATTGTGGTTGAACATGATTATGCTGAGTGCACTGGATCTGCTATTCAAGCTTTAGTTTTGTTTAAGAAGC
|||| | | || | ||| | | ||| |||| | ||||| | | | ||| || |||| || || | || | | | || | || ||| | | | ||| || | |||| | | ||| || | | | | ||| | | |
-----------gtaagattcttgataataaaccaactttcttttc--taactttgctagctttaacatccttgga--gactaacaaaacaatgatgcagGTA--TGTTGAGTGCACTGCATCAGCAA---TTCAGGCTCTAGTTTTGTTTAAGA-AGTTATACCTGGGACACAAGAAGAAGGAGATAGAC---AATTTCATCACAAAT--
upper sequence: GLYMA03G27660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 17
gtaagtattatataagttaataatgcatgcaacaagtacatattcattaaccgataaaaaaaagtcatccattaattaataaactaatcaattttgtcattactttttagATACTCAATCCCACAGAATTTTTAGGGAACATTGTGGTTGAACATGATTATGCTGAGTGCACTGGATCTGCTATTCAAGCTTTAGTTTTGTTTAAGAAGC
|||| | | ||| | ||| | | ||| |||| | | | ||||| | | ||| || | || | || || ||| ||| || || ||| | | | ||| || | |||| | ||| ||| | | | | ||| | | |
-----------gtaagattcttgatcatagaccaactttcttttc--taactctactagatttaacttccatgga--gactaacaaaacgatgatccagGTATGTTGAGTGCACTGCATCAGCCA-----TTCAGGCTCTAGTTTTGTTTAAGA-AGTTATACCCCCGACACAGGACGGAGGAGATAGAC---AATTTCATCACAAAT--
upper sequence: GLYMA03G27660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtattatataagttaataatgcatgcaacaagtacatattcattaaccga-taaaaaaaagtcatccattaattaataaactaatcaattttgtcattactttttagATACTCAATCCCACAGAATTTTTAGGGAACATTGTGGTTGAACATGATTATGCTGAGTGCACTGGATCTGCTATTCAAGCTTTAGTTTTGTTTAAGAAGC
||| | | || | || | | | | || | || | | ||| ||| || || | || || | | | || | || ||| | | | ||| || | |||| | | ||| ||| | | | | ||| | | |
----------------gtaagattcttgataatagaccttcttttctaactctactagatttaacttccttggagactaacaaaacgat-gatccagGTAT-----GTTGAGTGCACTGCATCAGCAA---TTCAGGCTCTAGTTTTGTTTAAGA-AGTTATACCCCGAACACAGGACGGAGGAGATAGAC---AATTTCATCACAAAT-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaaagtcatccattaattaataaactaatcaattttgtcattactttttagATACTCAATCCCACAGAATTTTTAGGGAACATTGTGGTTGAACATGATTATGCTGAGTGCACTGGATCTGCTATTCAAGCTTTAGTTTTGTTTAAGAAGC
aactaat putative branch site (score: 2)
ttacttttt putative PPT
attaattaataaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtattatataagttaataatgcatgcaacaagtacatattcattaaccgataaaaaaaagtcatccattaattaataaactaatcaattttgtcattactttttagATACTCAATCCCACAGAATTTTTAGGGAACATTGTGGTTGAACATGATTATGCTGAGTGCACTGGATCTGCTATTCAAGCTTTAGTTTTGTTTAAGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC