Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcaattttcctattatgtatttcagtatttctgttcttccaatgcacattcatttgttttttacttcataaaatctatcccacattgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT
Basic information
species | Glycine max |
transcript | GLYMA10G21350.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G047310_T02 (Zea mays), 3'ss of exon 6
gtaaggcaattttcctattatgtatttcagtatttctgttcttccaatgcacattcatttgttttttacttcataaaatctatcccacattgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT
|| ||| | | |||| | | || | |||| || ||| ||| ||||| | | || || ||| | | |||| ||||| ||| || | | ||||||||||| |||||||| |||||||| ||||| |||||||| || |||||||| || | ||||| |||||| |
gtgagggatatacgatatttggattggcaatttttccgtc-------tgcctatttttttgtctctatttttatgg--tcttttttatgc--cagATGATGGGAAACTACAAGCAGAGTCAGACTCTGGTGAATTCTGGGTCCTTTTTGGAGGTTTTGCACCAATTGGGAAAAAAACTGTGAGTGATGATGATGT
upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G180988_T01 (Zea mays), 3'ss of exon 6
gtaaggcaattttcctattatgtatttcagtatttctgttcttccaatgcacattcatttgttttttacttcataaaatctatcccacattgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT
|| ||| | | || ||| | | | | || || || || || || | | | | | | || | | | || |||| ||||| |||||| | | ||||||||||| |||||||| |||||||| ||||| |||||||| || |||||||| || | ||||| |||||| |
gtgaggga---tatataatatttggattggcaatt-tggtcgtctg--gcttttttctctatctctattcttatggggttttt-----atgccagATGATGGGAAATTACAGGCAGAGTCAGACTCTGGTGAATTCTGGGTCCTTTTTGGAGGTTTTGCACCAATTGGGAAAAAAACCGTGAGTGATGATGATGT
upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------gtaaggcaattttcctattatgtatt--tcagtatttc---tgttcttccaatgcacattcatttgttttt--tactt-------cataaaatctatcccacattgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT
| | || | | | || || ||||| || | |||| || ||| || || |||| |||| | | | ||| |||| |||||||||||||| || || ||||| || || || || |||||||||||||| || |||||||| || | | ||| || ||||||||||| ||
gtaagttgtattagacgcattacaactaatatttgaatatcttctttttcacgttttgatcagtcaatcaagcagcagttggatgctcaatcaatttattgcggtactcatgcatgtataataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT
upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 5
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------gtaaggcaattttcctattatgtattt-cagtatttctgttcttccaatgcacattc-atttgtt----ttttacttcataaaatctatcccac-attgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT
| || ||| | | | || |||| ||| | ||| | | || | ||| || || || | || ||| | || |||| || ||||||||||| || || ||||| || |||| |||||||||||||||||||||||||||||| || || | ||| || || ||| ||||| ||
gtaagccaattgcaccttcttcctcagtttcctttaagtcaatgaacagtgttttaatacttaaagaataggttttgtgtgtggaaacttatctatattcatactttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------------------gtaaggcaattttcctattatgtatttcagtatttctgttcttccaatgcacattcatttgtttt--ttactt--cataaaatctatcccacattgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT
||| |||| | | | | | |||| ||||| || | | | | || || || | |||| | | || |||| |||||||| | | ||||||| |||||||||||||| |||||||| ||||||||||||||||||||||| || ||||| || || |||||| |
gtaagagcacatgcattaataacttgctgatgttagcttcgcttttagtacttatgtatt-caatctctgaacagagctcatttgcattttcattcttaacatttgtaattgctactcttcattcattaacgtaaatgatgtttgcaatgccagATGATGGAAAGCTGGTTGCTGAGTCTGACTCAGGTGAATTCTGGGTCCTGTTTGGTGGTTTTGCTCCCATTGGCAAAAAGGTTGCCACCGAAGATGATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttccaatgcacattcatttgttttttacttcataaaatctatcccacattgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT
tctatccc CT-rich tract
attcatttgtttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcaattttcctattatgtatttcagtatttctgttcttccaatgcacattcatttgttttttacttcataaaatctatcccacattgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG