Sequence
atgc intronic sequence ATGC exonic sequencegttctttgctaatttaattggctaagttcataaacatgtgtccgctatggcttttaatttttaactgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
Basic information
species | Glycine max |
transcript | GLYMA20G35600.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 3'ss of exon 6
gttctttgctaatttaattggctaagttcataaacatgtgtccgctatggcttttaatt--tttaactgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
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----------gtttgtctttgttagctgaatcagtatgtcttccttggtgacattaatcagctgacgtgttcaacat-gcagGCTGAGAGCCTTAACATTAGTAGAGATGTCTCCGGTGAAGGTGTCCAGCAGGCTTTGTTGAAAATGCTGGAAGGCACA
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G050186_T03 (Zea mays), 3'ss of exon 5
gttctttgctaatttaattggctaagttcataaacatgtgtccgctatggcttttaatttttaactgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
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---gtatgtcatatcaatc--tttggcttggattttccctcctggtgtgggcgttgattagtttgtgatttggcatgcagGCTGAAAGTCTTAACATTAGCAGAGACGTATCTGGTGAAGGTGTTCAGCAGGCATTGCTGAAAATGCTGGAAGGCACG
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G101791_T01 (Zea mays), 3'ss of exon 6
gttctttgctaatttaattggctaagttcataaacatgtgtccgctatggcttttaatttttaactgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
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gtatgacatcaatct--ttggcttgaatttt-----ccctcctggtgtggacattcattagtttgtgatctggcatgcagGCTGAAAGTCTTAACATCAGCAGAGACGTATCTGGTGAAGGTGTTCAGCAGGCATTGCTGAAAATGCTGGAAGGCACG
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 6
----gt-tctttgctaatttaattggctaagttcataaacatgtgtccgctatggcttttaatttttaactgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
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gtcagtatgcaagacatgataacttctgaactcgataagaagaagataattgggctttatgcttcctggattctcctttctacagGCTGAGAGTTTAAACATTAGCCGGGATGTTTCTGGGGAAGGTGTTCAACAGGCACTTTTGAAATTACTGGAAGGCACT
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 6
--------gttcttt-gctaatttaattggctaagttcataaacatgtgtccgc-tatggcttttaattt--ttaactgttaaa---tattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
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gttccacagttttccagcttatttatttatttttatttaaatttaggtgtctttgtaaaaccaaaagtgcacttaaatgtggaaaccttttgcagGCTGAGAGCTTAAACCTTAGCAGAGATGTTTCTGGTGAGGGTGTTCAGCAAGCATTACTGAAAATGCTGGAAGGAACT
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S163_100V6.1 (Physcomitrella patens), 3'ss of exon 6
--------gttctttgctaatttaattggctaagttcataaacatgtgtccgcta--tggctttt----aatttttaac------tgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
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gagtccctgttcttagttacttctcaggagtaggagcacattgatacctcctcttccttgctttctaaaaatcattaacaatatgtatttgattgttcagGCGGAGAATATGAACATTAGCAGGGATGTATCTGGTGAAGGAGTTCAGCAGGCACTTTTGAAGATGCTGGAAGGAACT
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------gttctttgctaatttaattggctaagttcataaacatgtgt-----ccgctatggcttttaatttt--taactgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
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aaccgtttctgcccttttctactgactttcacgccctcagttataattttctttgaatgcagcttcgcaactcaatactgacactcagtgtatggttcagGCTGAGAGTAAAAATATTAGTCGGGATGTATCTGGTGAAGGTGTTCAGCAGGCACTATTGAAGATGCTTGAAGGCACT
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S171_84V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------gttctttgctaatttaattggctaagttcataaacatgtgtccgct---atggcttttaatttttaactgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
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tccctagttaaaagctggtccttatcatgtagcaattattatatcattggctgtgaatccacccgcatagtttagtattgacaacgtttggttgatccagGCAGAGAGTGTGAGCATTAGCCGAGACGTATCTGGTGAAGGCGTTCAGCAGGCGCTATTAAAGATGCTGGAAGGGACTMapped 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|193456440|gb|FK421786.1|FK421786EST: CTCAACAAGGGATTGTTTACATTGATGAAGTGGACAAGATAACTAAGAAG GCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAG
genomic: CTCAACAAGGGATTGTTTACATTGATGAAGTGGACAAGATAACTAAGAAGgttctttgct ... aatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAG
EST:
gi|17519864|gb|BM188906.1|BM188906EST: GATTGTTTACATTGATGAAGTGGACAAGATAACTAAGAAG GCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAG
genomic: GATTGTTTACATTGATGAAGTGGACAAGATAACTAAGAAGgttctttgct ... aatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcataaacatgtgtccgctatggcttttaatttttaactgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
ttttaac putative branch site (score: 2)
ttttaatttttaactg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctttgctaatttaattggctaagttcataaacatgtgtccgctatggcttttaatttttaactgttaaatattacagGCTGAGAGCTTGAATATTAGCCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTAAAAATGCTGGAAGGAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA