Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
Basic information
species | Glycine max |
transcript | GLYMA11G36000.3 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g07570.3 (Oryza sativa), 3'ss of exon 5
---------gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
|| ||| | | | ||| || || | ||| || || | | || || | | | ||| | ||| ||| ||| ||||||||||||| || |||||||| ||||| || ||||| || ||||||||||| || || | ||||||||||
gtgctttccttattccttttctcttttccatgatcgcatcattattagtttatactaataaagccctgttaacactttgc--ctcttcatccttgtaa--tccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGATAAAACCACCAATGTGCTTTACAAGGGATGATGCAG
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 7
lower sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
|||| || | | | ||||| || | | | || || || ||||| | || | | || | ||| | ||| || || ||||| || ||||||||||| || ||||| || ||||| ||||| |||||||||||||||||||| |||||||||||||
gtaaacaacat--taaagccaaaagcatcgatttgataagcatcagtt-----ggttaaccaaaatgtt----ttgctcctttctcttaat-gaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactc-ctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
| ||| | | || | || ||| | || || | ||| || || | || | |||| | | | || ||||||| |||||||||| | ||||| ||||| || ||||||||||| || || || |||||||| ||||||||||||||||||||||| |
-----------gtttgcaactccaccat-gattaagaaaaaattaattgtaa----tttaccaa-cacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 7
lower sequence: PP1S32_198V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------gtaagaaatttggttgaa----taaaaagaattgcatatgaagcttt-cttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
|| || ||| || | | | | ||| || ||| | | ||| | ||| | ||||| || ||| | ||| ||| ||||| || ||||||| || || ||||| ||||||||||| ||||| |||||||| || ||||||||| | | || |||||||
gtgatgctgcacttcacctagggctggcctagttctgtgtatcactagcaagttttgtactgctccttgacatggtggcaagtggggctgtgcaactcctaccattcacttacgcatag--gcttttt------ggatgttgcagACCTCGGAGTTTTAGTTGGGAAGGGCGGGCTTCATGGAAATGTCTTTAGAATCAAGCCTCCTATGTGTTTCTCAATGGAAGATGCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|16341987|gb|BI967582.1|BI967582EST: GAAGACACCTGCAAAGGCTGAAACAACAGCATTGCACGAAAGATTCAGAG AGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGA
genomic: GAAGACACCTGCAAAGGCTGAAACAACAGCATTGCACGAAAGATTCAGAGgtaagaaatt ... taaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGA
EST:
gi|6726423|gb|AW310777.1|AW310777EST: GAAGACACCTGCAAAGGCTGAAACAACAGCATTGCACGAAAGATTCAGAG AGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGA
genomic: GAAGACACCTGCAAAGGCTGAAACAACAGCATTGCACGAAAGATTCAGAGgtaagaaatt ... taaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
tagtaac putative branch site (score: 1)
ctcctat putative PPT
aaaatttctacaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG