Sequence
atgc intronic sequence ATGC exonic sequence...ttgttcaaaccaaaaaagtatctatttgattggcatacacctttagtttgatcaatataatagactttgtcccatccccttttgttgttttctttaccagAATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCAAAG
Basic information
species | Glycine max |
transcript | GLYMA19G42530.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 23
--------ttgttcaaaccaaaaaa-gtatctatttgattggcatacacctttagtttgat-caatataatagact-ttgtcccatccccttttgttgttttctttaccagAATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCAAAG
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gtataaaattgctctcattgtcttgcatttatatttatttgagaaacacatttgctcagaagtgtttttgtccattgttgtttaatcttcttctaa-actttcttt-ccagAATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAG
upper sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 13
ttgttcaaaccaaaaaagtatctatttgattggcatacacctttagtttgatcaatataataga-ctttgtcc-------catccccttttg-----ttgttttctttaccagAATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCAAAG
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-----------------gtatgaatttggttc-cacattctcttcatgtta-caacataaaaaatccttgtctgtaaaattgttggtttctaaaattctttttgttttgtcagAATTTGGATTCCAAGATTCATCACAACAACCTTCTCAATAACATACTAGCAAAG
upper sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 23
--------ttgttcaaaccaaaaaagtatctatttgattggcatacacctttagtttgatcaatataatagactttgtcccatccccttttgttgttttctttaccagAATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCAAAG
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aaaatatttagtttaatctcaaccacaatttttatgtggtggatatattctta--tttgctgatgtaattgaccctgatttattttcttttgta------ccaaccagAATTTGGATTCAAAGATTCACCATAATAACCTTCTTAACAACATACTTGCAAAGMapped 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|23064265|gb|BU579038.1|BU579038EST: GACGTGGTATAGTTCTTGTAACAGCCACAACGCGCCGTAATTCACCTAAT AATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCA
genomic: GACGTGGTATAGTTCTTGTAACAGCCACAACGCGCCGTAATTCACCTAATgtaagttttt ... tctttaccagAATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgatcaatataatagactttgtcccatccccttttgttgttttctttaccagAATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCAAAG
gtttgat putative branch site (score: 5)
ctttgtcccatcccct putative PPT
aatataatagacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttcaaaccaaaaaagtatctatttgattggcatacacctttagtttgatcaatataatagactttgtcccatccccttttgttgttttctttaccagAATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - tcaaacc
- - - - - -aaaaaag
- - - - - - - - - - - - - - - - -catacac