Sequence
atgc intronic sequence ATGC exonic sequence...tttaaaatatattgtgctgtactagagataaaataataactttttatttctagtgtccacttttctatgaaagtcaactgttttttgtgttgatttatagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
Basic information
species | Glycine max |
transcript | GLYMA09G32050.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G32050.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g11820.1 (Oryza sativa), 3'ss of exon 3
-----------tttaaaatatattgtgctgtactagagataaaataataactttttatttctagtgtccactt----------------ttctatgaaagtcaactgtttt--ttgtgttgat-----------------ttatagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
|| | | | || || | ||| | ||| | | || | || | | ||||| || || || |||||| | | || | ||||| || |||||| || ||||| ||||||| || |||||||| |||||||| |||||| |||| |||||||||||||||||||||||||| ||| ||
gtaagattcttattcagttctgttttgttacacttgtaatatgtcga-acctctctagcttcactgtccctttggtcaaattagatgcattttagtgaagtcagtgatcctaattttattgatgacaaaatttgttttgcttctagCCGAGAGTTCACGCATCGAGCGAAGTCAGTTTCTATGGCTAAATTTACTGCACAGGAAGTTAGTGCCCTTCAAGAAGGAGGAAATGAG
upper sequence: GLYMA09G32050.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g45840.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------------tttaaaatata-ttgtgctg-tactagagataaa--ataataactttttatttct-------agtgtccacttttctatgaaagtcaactgttttttgtg------ttgatttatagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
|| ||||| | || | |||| | ||| | || | || | | |||| | ||| | | || || || || || || || | | || ||||| ||||||||||| ||||||||| | ||||||||||| |||||||| ||||||||| ||| ||||||||||| || || ||
gtaagtggtgaaaatatccttctagtgtttcctctgtttcttactttaaaaatgcaattccacaactacttgtgattgactatgacaattatgaatttatgtgcagaagtaataaactcctgataaatgttgtctaattactgaactttaattattcttcagTCGGGAGTTCACTCATCGTGTAAAATCAATATCAATGGCTAAATTTACTTCTCAAGAAGTTTCTGCTCTTCAAGAAGGGGGAAACGAG
upper sequence: GLYMA09G32050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 4
--------------------------------------------------------tttaaaatatattgtgctgtactagagataaaataataactttttatttctagtgtccacttttctatgaaagtcaactgtttt-----------ttgtgttgattta-tagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
|| | | || | ||| | || | | | | || || | | | | | | | || |||| | ||| ||| ||| ||||| ||||| |||||||||||||| ||||| ||||| || |||||| |||||||||||| ||||||||||||||| |||||| ||
gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtgaattattgggcacaccagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
upper sequence: GLYMA09G32050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------tttaaaatatattgtgctgta--ctagagataaaataataactttttatttctagtgtccacttttctatgaaagtcaactgtttttt-----gtgttgat----------ttatagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
| | | | | | | | || ||| | |||| | | | | || | | | | | || | || ||||| | | ||| || ||| ||||| || || |||||||||||||| ||||| ||||| || ||||| ||||||||||| ||||||||||||||| |||||| ||
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
upper sequence: GLYMA09G32050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G136547_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------tttaaaatatattgtgctg-tactagagataaaataataactttttatttctagtgtccacttttctatgaaagtcaa-------ctgttttt----tgtgttgatttatagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
|| | | |||| | || || || | | | || ||| | | | |||| | | | | | | ||| | |||| |||| ||||| || |||| |||||| ||||||||||| ||||||||||| || ||||| ||||||||| || |||| |||||| || ||| ||
gtaagtggtgatcatattgttgtttttctctttattaaaagtgcagcaatgtttcttgtttggctattacagttgtga--actcctccctataagttatataaacttctgaaccagtgcctgtgcttgcccatttctgaattgtgacattttacagCCGAGAGTTCAGTCATCGTGTAAAATCAGTATCAATGGCTAAATTCACTTCCCAAGAAGTTTCGGCACTTCTAGAAGGGGGCAATGAG
upper sequence: GLYMA09G32050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G126079_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------tttaaaatatattgtgctg-tactagagataaaataataactttttatttctagtgtccacttttctatgaaagtcaa-------ctgttttt----tgtgttgatttatagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
|| || | |||| | || || || | | | || || | | | |||| | | | | | | ||| | ||| |||| ||||| || |||| |||||| ||||||||||| || |||||||| || ||||| ||||||||| || ||||| ||||| || ||| ||
gtaagtggtgatcatattgttgtttttctctttattaaaagtgcagcaatatttcttgtttggctattacagttgtga--actcctccctacaagttatataaacttctgaaccagtgcctgtgcttgcccatttctgaatcgtgacattttacagCCGAGAGTTCAGTCATCGTGTAAAATCAGTATCGATGGCTAAATTCACTTCCCAAGAAGTTTCGGCACTTCAGGAAGGGGGCAATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctagtgtccacttttctatgaaagtcaactgttttttgtgttgatttatagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
tgttgat putative branch site (score: 4)
ttgatttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaaaatatattgtgctgtactagagataaaataataactttttatttctagtgtccacttttctatgaaagtcaactgttttttgtgttgatttatagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - tgctgta
- - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtg