Sequence
atgc intronic sequence ATGC exonic sequencegtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaattaatgacgttttttttggtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
Basic information
species | Glycine max |
transcript | GLYMA13G02510.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g36480.1 (Oryza sativa), 3'ss of exon 1
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaattaatgacgttttttttgg-tgtctccttgt-agGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
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--------------------------------------------------------gtaacgtatttaccattcattcatgcatgtgtaaaacacattttaccgttc-atgcgaata--tgtatgtactgagttgagttctgactcgatcgaacaaatgctcatcagCGTGGTGGTACAAGCCAGAGTACATCATCAACGAGCTGAACGTGAACTCGGTGATCACGACGCCCGGGCACGACGAGATCCTGCCCATCAACGGCATCAC
upper sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g36500.1 (Oryza sativa), 3'ss of exon 1
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtg-agatttagataatttcatggacagaaattaatgacgttttttttgg-tgtctccttgt-agGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
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----------------------------------------------------------------------gtaacgt--atatttaccatgcgtgcatgcgtaaaacacattttaccgttcttgcgaatatgtatgtatactgactcgatcgaacaaatgctcatcagCGTGGTGGTACAAGCCGGAGTACATCATCAACGAGCTGAACGTGAACTCGGTGATCACGGCGCCCGGGCACGACGAGATCCTGCCCATCAACGGCATCAC
upper sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaattaatgacgttttttttggtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
||||| || | || | | |||| ||| | | || | | ||| | || | | | | || ||||||||| | | || || ||||||||||||||| || ||||| || |||||| |||| |||||||| ||||| || ||||| | ||||| ||| | | |||||||| | |||
----------------------------------gtaattaaccaaccatatcttcctcgaacgcactgcacgagac-----acacattgttgcatctttg--------------tgatctta---------acttgtg-tgttttttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
upper sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G568636_T01 (Zea mays), 3'ss of exon 1
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaattaatgacgttttttttg-gtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
| | || || | | | | | | | | || | | || |||| || | ||| | | || |||||||||||||| || ||||||||||||||| |||| |||||||| |||||||| ||||| | ||||| |||||| ||||||||||| ||
----------------------------------------------------------------------------------gtaattagcagttcatgtttaatttattactactcaag-caaaaaaaatgatgtctgactttgctattgcaaatgattgagcagCGTGGTGGTACAAGCCGGAGTACATCATCAACGAGCTGAACATAAACTCGGTGATAACGACGCCGGGGCACGACGAGATCCTGCCCATCAACAGCATTAC
upper sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G076723_T01 (Zea mays), 3'ss of exon 1
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaatta-atgacgttttttttggtgtctcctt-gtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
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---------------------------------------------------------------------------gtaactagtgtttgtttgtttgtttactacggatcggaagcaaagcaagcaagcgaaacgggattttgatcttgctgctgcaaaatgagcagCGTGGTGGTACAAGCCGGAGTACATCATCAACGAGCTGAACATAAACTCGGTGATAACGACGCCGGGGCACGACGAGATCCTGCCCATCAACGGCATCAC
upper sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G37130.1 (Arabidopsis thaliana), 3'ss of exon 1
--gtataatatgtcttt-cttcga--actcttatggtttttaattttgttacttcttttt---gcctaggaa--tattgcatgaggttgaaaatgaacagtggtacttttacagtgagattta---------gataatttcatggacagaaattaatgacgtttt---ttttggtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
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gtacataaaatctttttgcttcaataaatctcattaagatgaactaattgatatgtttaaaaagtctccgaacctataggagaaaaacaaaaacaga-aatcatattaaaaaatgaaaaactaatgttggtggatgatgtcagcttctgtgacttacataaattcaaattcaatggttttgttttagGTTGGTGGTATAAGCCAGAGTACATAATCAACGAGCTAAACATAAACTCCGTGATTACGACGCCATGTCACGAGGAGATTCTTCCCATCAACGCTTTCAC
upper sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G77760.1 (Arabidopsis thaliana), 3'ss of exon 1
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaattaatgacgttttttttggtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
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------------------------------------------------------------------------------------gtaaactattaacttacccttgtcttcttttacattttagttaccgatgctaatattatttactt--gt-ttttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC
upper sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 1
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaattaatgacgttttttttggtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
| | | | | |||| |||| ||||| | | || | | ||||| | | |||| | ||| | ||||| | |||| | || | | || ||||||||| ||||| || |||||||| || ||| |||| || ||||| || || ||||| || || ||||| || ||||| ||||||||||| |||||
---------------------------gtacactgcgccccacatccccccacccccctattaatag-acatgactctctatattt-tgtttttggttttataaatgggcgaagatga------ggatctgaggtaatgttactattttggttgacatggagcagCTTGGTGGTATAAGCCGGAGTACATCATTAATGAGCTGAACATTAACTCCGTCATCACTACACCATGCCACGAAGAAATCTTACCCATCAACTCCTGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagataatttcatggacagaaattaatgacgttttttttggtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
aattaat putative branch site (score: 3)
tgtctcctt putative PPT
agaaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaattaatgacgttttttttggtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA