Sequence
atgc intronic sequence ATGC exonic sequencegtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttattgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACTATTGATGATATACAAAAACTTCATATTCGCTCTATTCCGCTGGGGGAGCACGCACGACGT
Basic information
species | Glycine max |
transcript | GLYMA12G08330.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 4
gtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaattt-attgtaaaatcttttactggtgatgacactcatctactgttaataactgaaa---cagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACTATTGATGATATACAAAAACTTCATATTCGCTCTATTCCGCTGGGGGAGCACGCACGACGT
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----------------------------------tcatttgtgtcactggtctagtcattgtggagt----tacagttagaaagtattaccactgtcttaaggttcctctagttcacccttcttttttccaatgtcagTCTTGCAATTGCTAAAGAGGGTGAGCTTTCAATTGGAACTATTGATGATATCCAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGCCGC
upper sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 16
gtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttattgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACTATTGATGATATACAAAAACTTCATATTCGCTCTATTCCGCTGGGGGAGCACGCACGACGT
|||| | ||| | || | | || || | ||| | | ||| | | | |||| ||| || | | || | ||||| | | ||| || ||||| | |||||||| ||||| ||||| ||| | ||||| ||||| ||||||||||| || |||||||| ||| | || || || || || ||||| ||
-------------------tttgtgtcactggtccagtctttgtggag--ttatggt----ttgaaaatgataccact-gtcgtaag----tttgctctagttcac-cccatcttttttc--taa-tgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC
upper sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 16
gtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttattgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACTATTGATGATATACAAAAACTTCATATTCGCTCTATTCCGCTGGGGGAGCACGCACGACGT
| || ||| | || | | | | | || ||| | | || ||| || || | ||||||| ||| | | ||| ||| | |||||||| ||||||||||| ||||| || || || ||||||||||| || || ||||| || |||||||| || || |||||||| || || ||
------------ccatgagcttggtacaagtaagaggctgagaa----------gatgaaattgtaaatgatattattgg--gttaagagactaactggtggcttttctccccctttctta----------cagCCTTGCAATTGCCAAAGAAGGTGATCTTACAATCGGTACCATTGATGATATCCAGAAGCTTCACATCCGCTCTATCCCACTTGGGGAGCATGCTCGCCGC
upper sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 16
gtatcttggtctttgttagtttgacttactagagttgtttaca-tatccccttgtgctgttcttggatcttgtacaatttattgtaaaatcttttactggtgatgacactcatctactg---ttaataactgaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACTATTGATGATATACAAAAACTTCATATTCGCTCTATTCCGCTGGGGGAGCACGCACGACGT
| || | ||| | ||||| | ||| | || | || | ||| || | || | | || | | |||| | |||||| |||| | || || | ||| ||||| ||||| || || ||||| ||||||||||| ||||| |||||||||||| | |||| || || || | | | | |||
----------------------------------cagcatagaatattactttgtgtcatactttaaatttatg-aactagttg-aatacattaaagtaaggaccttcatgactgactgatttcgataacttc--cagTCTTGCCATCGGAAAGGAAGGGGAGCTCACAATCGGCACCATTGATGATATTCAAAAGCTTCATATTCGCACAGTTCCTCTTGGCGAACGCCCTTGCCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACTATTGATGATATACAAAAACTTCATATTCGCTCTATTCCGCTGGGGGAGCACGCACGACGT
taataac putative branch site (score: 1)
aaaatctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttattgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACTATTGATGATATACAAAAACTTCATATTCGCTCTATTCCGCTGGGGGAGCACGCACGACGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA