Sequence
atgc intronic sequence ATGC exonic sequence...tataaattttgtaacggtcaatatctgtttaagtacactatctcttatggtgtttcttctaatattcaatatgtgtattcttttcttctgaactcttcagGGTATGAGCCAACTTGAGCTGGAAGATGAGGTTCAAGACGATCTCAAACGTGCTACTGGGGAGTTTACCAAGGATGCAGATGATGCAAATAAGCTCAATC
Basic information
species | Glycine max |
transcript | GLYMA08G23780.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 3'ss of exon 1
----tataaattttgtaacggtcaatatctgtttaagtacactatctcttatggtgtttcttctaatattcaatatgtgtattcttttcttctgaactcttcagGGTATGAGCCAACTTGAGCTGGAAGATGAGGTTCAAGACGATCTCAAACGTGCTACTGGGGAGTTTACCAAGGATGCAGATGATGCAAATAAGCTCAATC
| | || | | | | | | | || || | ||| | | | || || | | || | | | | ||| | | ||||| ||||||||||||||| ||||||||| || ||||| ||| | || ||||||||| || ||||| || ||||||||||| ||||| | || ||||
tggactgacgtgttactatg-ttactgttttttcctgtctagtatttgaaaagatggc-ctgcggttctttcttcactaaaacatgccattc--attcttgcagGGAATGAGCCAACTTGAGTTGGAAGATGCAGTCCAAGATGATTTGAAGGCTGCTACTGGTGAATTTACAAAAGATGCAGATGACGCAAACAGACTGAATC
upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G378906_T01 (Zea mays), 3'ss of exon 1
tataaattttgtaacggtcaatatctgtttaagtacactatctcttatggtgttt-cttcta-atattcaatatgtgtattcttttcttctgaactcttcagGGTATGAGCCAACTTGAGCTGGAAGATGAGGTTCAAGACGATCTCAAACGTGCTACTGGGGAGTTTACCAAGGATGCAGATGATGCAAATAAGCTCAATC
|| |||| || | | || | | | | | | ||| || | ||| | |||| | | | | | || || || | |||| |||||||| |||||| ||||||||||||| || || ||| | || ||| ||||| | |||||| |||||||||||||||||||| |||||||| |
ctggtgttgtgtattgggct-tggatgataccttgccacttttagtgtggccttcacatctgtaccttcagttattaaagcatgctattttgttatcat-agGGCATGAGCCAGCTTGAGTTGGAAGATGAGGTGCACGATGATTTGAAGGCTGCAACTGGTGGGTTTACTAAGGATGCAGATGATGCAAACAAGCTCAACC
upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 1
------tataaattttgtaacggtcaatatctgtttaagtacactatctcttatggtgtttcttctaatattcaatatgtgtattcttttcttctgaactcttcagGGTATGAGCCAACTTGAGCTGGAAGATGAGGTTCAAGACGATCTCAAACGTGCTACTGGGGAGTTTACCAAGGATGCAGATGATGCAAATAAGCTCAATC
| | || || | | | | || | | | | | ||| | ||| ||| | | | || | || || || || | | |||| |||||||| |||||| ||||||||||||| || || ||| | || ||| ||||| | ||||||||||||||||||||| ||||| |||||||| |
gtctggtgttgtcttggtt-tgcacgacaccttgccacttctagtgtggctt-tcacatttgctctttcagttattaaa-gcatgctatttttgttgtcat---agGGCATGAGCCAGCTTGAGTTGGAAGATGAGGTGCATGATGATTTGAAGGCTGCAACTGGTGGGTTTACCAAGGATGCAGATGACGCAAACAAGCTCAACC
upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0018g02080.t01 (Vitis vinifera), 3'ss of exon 1
tataaattttgtaacggtcaat-atctgtttaagtacactatctcttatg---gtgtttcttctaatattcaatatgtgtattcttttcttctgaactcttcagGGTATGAGCCAACTTGAGCTGGAAGATGAGGTTCAAGACGATCTCAAACGTGCTACTGGGGAGTTTACCAAGGATGCAGATGATGCAAATAAGCTCAATC
| | || || | | || | || | | | || || || || | | ||| || || ||| | || | | ||||||||||||| ||||| |||||||||||||| ||||| ||||||||| |||||||||| | ||| || ||||||| |||||||| |||||| || ||||
----actctttaaatatttggtcatggaatctagaaagccccatattgtgtttgtaaacattttgagtttcttgattacagtttgtttgcacataattttctagGGTATGAGCCAGCTTGAACTGGAAGATGAGGTGCAAGATGATCTCAAATGTGCTACTGGAGGGTTCACAAAGGATGGAGATGATGTAAATAAACTTAATC
upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ09162 (Selaginella moellendorffii), 3'ss of exon 1
tataaattttgtaacggtcaatatctgtttaagtacactatctcttatggtgtttcttctaatattcaatatgtgtattcttttcttctgaactcttcagGGTATGAGCCAACTTGAGCTGGAAGATGAGGTTCAAGACGATCTCAAACGTGCTACTGGGGAGTTTACCAAGGATGCAGATGATGCAAATAAGCTCAATC
| ||| ||| | ||| ||||| | || ||||| ||||||||||| ||||||||||| |||||||| ||||| || || |||||||| ||||| ||||| || || || | || ||||| || |
-------------------------------------------------------gtcttaactgacaacgc-tctatcgttttcgtttg------ccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGAGCTACTGGAGAGTTCACCAAAGACAGCGACGACACCAAGAAGCTGAACC
upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ07199 (Selaginella moellendorffii), 3'ss of exon 1
tataaattttgtaacggtcaatatctgtttaagtacactatctcttatggtgtttcttctaatattcaatatgtgtattcttttcttctgaactcttcagGGTATGAGCCAACTTGAGCTGGAAGATGAGGTTCAAGACGATCTCAAACGTGCTACTGGGGAGTTTACCAAGGATGCAGATGATGCAAATAAGCTCAATC
|| || |||| | | |||| | | | | || | | | ||||| ||||||||||| ||||||||||| |||||||| ||||| || || |||||||| ||||| ||||| || || || | || ||| | || |
--------------------------------gttagctctctcccctctttcctcttgcacgtcttagctgacaacgctctatcgttttcgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGAGCTACTGGAGAGTTCACCAAAGACAGCGACGACACCAAGAAGTTGAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggtgtttcttctaatattcaatatgtgtattcttttcttctgaactcttcagGGTATGAGCCAACTTGAGCTGGAAGATGAGGTTCAAGACGATCTCAAACGTGCTACTGGGGAGTTTACCAAGGATGCAGATGATGCAAATAAGCTCAATC
ttctaat putative branch site (score: 2)
ttcttttcttctgaac putative PPT
ttctaatattcaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tataaattttgtaacggtcaatatctgtttaagtacactatctcttatggtgtttcttctaatattcaatatgtgtattcttttcttctgaactcttcagGGTATGAGCCAACTTGAGCTGGAAGATGAGGTTCAAGACGATCTCAAACGTGCTACTGGGGAGTTTACCAAGGATGCAGATGATGCAAATAAGCTCAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - -tatggtg