Sequence
atgc intronic sequence ATGC exonic sequencegtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttctttttttaagtttttgcatagtcacatagttaacaaaattgagctttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
Basic information
species | Glycine max |
transcript | GLYMA12G35840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttctttttttaagtttttgcatagtcacatagttaacaaaattgagctttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
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-----------------gtgagttacagaaacaata----ctatgatatcaaacatcctatggtttctt----atcatctaattgtgaaa---------------tttcaaatataatttagGATAAGGAATTGTTTGGTTCAACTATACTCAAAGGATATCACACCAGATGATAAACAGGAGCTTGATGAGGCTCTCCAGAGGGAG
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttctttttttaagtttttgcatagtcacatagttaacaaaattgagctttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
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------------------------------------gttagtttgccaaccagtgcattgtagttgacatgca-caacttcgtt--cagcctttaatctt--gatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAG
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttctttttttaagtttttgcatagtcacatagttaacaaaattgagctttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG---------------
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------------------------------------gttagtttgccaaccagtgcattgtagttgacatgca-caacttcgtt--cagcctttaatctt--gatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttctttttttaagtttttgcatagtcacatagttaacaaaattgagctttatggttttcatctgcat-tgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
|| | ||| || ||| |||| | || | | | || | | | | || |||| | | || || ||| ||| ||| || || ||||||||||| || |||||| ||||| | ||||| || ||||| ||||| ||||| || ||||| |||||||| || || ||||| |||
--atgaaaagaaaagtaatatatttctcgagtcatgttgaaccatatgttatatgtgcc--atttgttgcct---tagattcttcaca----------------tttgcatttgaatgtgcagGATAAGAAACTGTTTAACTCAACTTTATGCAAAGGACATCACTCCAGATGAGAAACAGGAACTTGATGAAGCACTTCAAAGAGAG
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttctttttttaagtttttgcatagtcacatagttaacaaaattgagctttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
||| | | | | || | || | | ||| ||||| || | | || || | || | | ||| ||| | |||||| |||| |||||| | || || ||||||||||||||||||||||||||||||||||| ||||||||||||||||| || |||
---------------------gtttgtaatcaaattcctgcccttttgttcttgcactataattttttc-----tctccttttt-------ttcacctctcttatttct-tctact---cagGATCCGGAACTGTTTAGCCCAGTTATATGCCAAAGACATTACTCCTGATGATAAGCAGGAACTTGATGAGGCTCTACAGAGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatagtcacatagttaacaaaattgagctttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
agttaac putative branch site (score: 3)
ttttcatct putative PPT
atagttaacaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttctttttttaagtttttgcatagtcacatagttaacaaaattgagctttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT