Sequence
atgc intronic sequence ATGC exonic sequencegtagttcattcattgttgcattttttatacatttgaaaatggaaatcattgacctgtaatgacaggacatgatatatatagactatagtataccatttctggcattgtggcaatttctgcattgagactaattatttctgttggtgatcattctcttcaggataaagGAATTTGTTTGACACAATTATATGCTAAGGACATTACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
Basic information
species | Glycine max |
transcript | GLYMA13G36670.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 2
gtagttcattcattgttgcattttttatacatttgaaaatggaaatcattgacctgtaatgacaggacatgatatatatagactatagtataccatttctggcattgtggcaatttctgcattgagactaattatttctgttggtgatcattctcttcaggataaagGAATTTGTTTGACACAATTATATGCTAAGGACATTACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
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--------------------------------------------------------------------gtgagttacagaaacaatactatg--atatcaaacatccta-tggtttctt-------atcatctaattgtgaaatttcaaatataatttagGATAAGGAA--TTGTTTGGTTCAACTATACTCAAAGGATATCACACCAGATGATAAACAGGAGCTTGATGAGGCTCTCCAGAGGGAG
upper sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 2
gtagttcattcattgttgcattttttatacatttgaaaatggaaatcattgacctgtaatgacaggacatgatatatatagactatagtataccatttctggcattgtggcaatttctgcattgagactaattatttctgttggtgatcattctcttcaggataaagGAATTTGTTTGACACAATTATATGCTAAGGACATTACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
| | | ||| | | || ||| ||| ||| || || || ||| | || | || ||||| |||||||| | |||||| ||| | || | || || || || || ||||||||||||||||||||||||||| | |||||||||
-----------------------------------------------------------------------gttagtttgccaaccagtgcattgtagttgacatgc--acaacttc---gttcagcct--ttaatcttgatcccaat-attcttatcagGATACGCAA--CTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAG
upper sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
gtagttcattcattgttgcattttttatacatttgaaaatggaaatcattgacctgtaatgacaggacatgatatatatagactatagtataccatttctggcattgtggcaatttctgcattgagactaattatttctgttggtgatcattctcttcaggataaagGAATTTGTTTGACACAATTATATGCTAAGGACATTACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG---------------
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-----------------------------------------------------------------------gttagtttgccaaccagtgcattgtagttgacatgc--acaacttc---gttcagcct--ttaatcttgatcccaat-attcttatcagGATACGCAA--CTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctgcattgagactaattatttctgttggtgatcattctcttcaggataaagGAATTTGTTTGACACAATTATATGCTAAGGACATTACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
gactaat putative branch site (score: 2)
tcattctcttc putative PPT
taattatttctgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttcattcattgttgcattttttatacatttgaaaatggaaatcattgacctgtaatgacaggacatgatatatatagactatagtataccatttctggcattgtggcaatttctgcattgagactaattatttctgttggtgatcattctcttcaggataaagGAATTTGTTTGACACAATTATATGCTAAGGACATTACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA