Sequence
atgc intronic sequence ATGC exonic sequence...atagatatattgtattataactaaaccatttgtataattttatcatctttgatttggttaatcatccttctggaatttatctttccaaatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
Basic information
species | Glycine max |
transcript | GLYMA11G35460.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 7
--atagatatattgtattataactaaaccatttgtataattttatcatctttgatttggttaatcatccttctg--gaatttatctttccaaatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
||| | | || ||||| | | | | || | | |||||| | |||| | | |||| | | || |||||||||| ||| ||||||||||| ||||| ||||||||||| || ||||||||| ||||||||||| || |||||||||
attccaccccattcttctccttgtaggccattaacagtgaataaatgttcatg----gataaatcattcctctgttcactcgttcttcctatcatttatttcagGGAAACCAGGGTTTTCCAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTCAGGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 7
--atagatatattgtattataactaaaccatttgtataattttatcatctttgatttggttaatcatccttctg--gaatttatctttccaaatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
||| | | || ||||| | | | | || | | |||||| | |||| | | |||| | | || |||||||||| ||| ||||||||||| ||||| ||||| ||||| || ||||||||| ||||||||||| || |||||||||
attccaccccattcttctccttgtaggccattaacagtgaataaatgttcatg----gataaatcattcctctgttcactcgttcttcctatcatttatttcagGGAAACCAGGGTTTTCCAAGAAGCAAGCTGATCTCTTCTTCCCCCCAGATTTTCAGGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 7
atagatatattgtattataactaaaccatt--tgtataattttatcatctttgatttggttaatcatccttctggaatttatctttcca-aatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
||| ||||| | | | |||| ||| || | ||| || ||| | || |||| |||| | || ||||||||||| ||||||||| | || || || |||||||| || || || ||||||||||||||||||||||| || |||||||||
-------------gtta-gcttaaactactgctctatattttcatggttattg--ttagttggt-attagtctgatgtttaaaggtgggcggctttttttcagGGAAACCATCATTTACAAAAAAGCAGGCAGATCTCTTTTTCCCCCCAGATTTTGCTGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
atagatatattgtattataactaaaccatttgtataattt--tatcatc--tttgatttggttaatc--atccttctggaatttatctttcca-aatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
| | | ||||| | | | | | |||| ||| || || ||| | | || | |||| |||| | |||| ||| |||| || ||||||||| | || |||||||||||||| || ||||| || |||||||||||||||||||| ||||||||||||
gttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgttttctaggttgtattcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 7
atagatatattgtattataactaaaccatt-tgtataattttatcatcttt--gatttggttaat-catccttctggaatttatctttccaaatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
|| | | | | || |||| ||| |||||| | ||| ||| ||| | | | | || ||| |||||||| ||||||| ||| |||| | |||||||| || |||||||||||||||||||||||||||||||||||||||||||| ||||||
---gactcactactct-tggtggaatcattatgttaccttttattttgttttgaattctgttcttatgtttattcctgttctaacttcaataatttcttagcagGGAAACCAGGATTTACAAAGAAACAGGCTGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCAATGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 8
-atagatatattgtattataactaaaccatttgtataatttt-atcatctttgatttggttaatcatccttctggaatttatctttccaaatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
| || || | | | | | || |||| | || || || || | ||| | |||| | | || ||| |||| | || ||| ||||||| || || | || |||||||| |||||||| || |||||||||||||| ||||||
tgtgaatggatacgaagagggtgatattgtcgttacaattaggaggatattatgaaaggccgttcgtaagcctg--acttatttcttatgcttgatttccagGTAGACCCGGGTTTGCCAAGAAGGCGGCGGACTTGTTTTTTCCTCCGGATTTTGCAGACGATTTTCCAGTTGCAATGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 7
atagatatattgtattataactaaaccatttgtataattttatcatctttgatttggttaatcatccttctggaatttatctttccaaat----ttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
|| || | | | || | | | | | || | || | | | | ||| | || | || | |||| |||| | || || |||||||| ||||||||| || ||||||||||||||||| ||||| ||||| ||| | ||||||
----ctacttttctccgttgttcagtgggaaatagcagcatgttggttgcgtttaatctcttctctcctattaattttttacttactcatgctatgctttgcagGTAGACCTGGTTTCTCCAAGAAGGCAGCAGATCTATTTTTTCCTCCAGATTTTGCCGATGACTTTCCCGTTTCGATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgatttggttaatcatccttctggaatttatctttccaaatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
ggttaat putative branch site (score: 4)
tttcttttc putative PPT
aatttatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagatatattgtattataactaaaccatttgtataattttatcatctttgatttggttaatcatccttctggaatttatctttccaaatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - ctaaacc
- - - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctg