Sequence
atgc intronic sequence ATGC exonic sequence...ataaatctgttgacccattaaaagggtacggacttgttatagtaggattctttatggctcacaatatttggatcattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
Basic information
species | Glycine max |
transcript | GLYMA04G41530.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 10
---------ataaatctgttgacccattaaaagggtacggacttgttatagtaggattctttatggctcacaatatttggatcattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
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agcttcagcattggtggcatcattttcccatacagttctagatatttaca-tatgattttaaattgttaaca-tatct-------taattgctatgatttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC
upper sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
----ataaatctgttgacccattaaaagggtacggactt-gttatagtaggattctttatggctcacaatatttggatcattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
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accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgtttt---ctgatgcatttttaactgtta--tggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
upper sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G06160.1 (Arabidopsis thaliana), 3'ss of exon 9
ataaatctgttgacccattaaaagggtacggacttgttatagtaggattctttatggctcacaatatt-tggat---cattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
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-------------------------gtatgtagtttattta-tgagaccattgttgtatcaaaggaacatagattcacattaaatttcttgttat--tacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
upper sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 10
ataaatctgttgacccattaaaagggtac-ggacttgttatagtaggattctttatggctcacaatatttggatcattaaataatataatatgtt--tttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
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-gctatgtgctaactgagaaagaagccattggagtttactttggggggacaattgtgaatagcc-tctatgga-ctttgaagactgcttttttttaatttcagGAATTCAAGTGTGAGATATGTGGGAATCACAGTTACTGGGGGCGTAGGGCTTTTGAGCGGCATTTTAAGGAATGGCGCCATCAGCATGGTATGCGTTGCC
upper sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S218_51V6.1 (Physcomitrella patens), 3'ss of exon 10
ataaatctgttgacccattaaaagggtacggacttgttatagtagga---ttctttatggctcacaatatttggatcattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
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-taagacgcttggccgtagaaatgaatttcggttctgcagtgtaggaccatctcttttttctcgcagc-tttgcacc-tggattgacgagtgataattttcagGAGTTTAAATGTGAGATATGCGGCAATTATAGCTATTGGGGTCGACGGGCTTTTGAACGACACTTCAAGGAATGGAGACATCAGCATGGAATGCGTTGTT
upper sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ22878 (Selaginella moellendorffii), 3'ss of exon 9
ataaatctgttgacccattaaaagggtacggacttgttatagtaggattctttatggctcacaatatttggatcattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
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-----------------------------------------gtaaaaa--gttatgctccttcttttgcaagccttcatctcctctcctttgttttgcagGAGTTCAAATGCGAGATATGTGGAAACTCCAGCTACTGGGGGCGAAGGGCCTTCGAACGACACTTCAAAGAATGGAGGCATCAGCACGGCATGCGCTGCTMapped 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|193378398|gb|FK345089.1|FK345089EST: CCTATACCTTACTGGCTGTATAAGCTACATGGTCTGGGTCAG GAATTTAAGTGTGAGATATGCGGGAACTACAGTTTATTGGGGGCGTCGGGC
genomic: CCTATACCTTATTGGCTGTATAAGCTACATGGTCTGGGTCAGgtattatatt ... tgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAG-TTATTGGGGGCGTCGGGC
EST:
gi|193451880|gb|FK419392.1|FK419392EST: TTATTGGCTGTATAAGCTACATGGTCTGGGTCAG GAATTTAAGTGTGGGATATGCGGGAACTACAGTTATTGGGGGCGTCAGGCT
genomic: TTATTGGCTGTATAAGCTACATGGTCTGGGTCAGgtattatatt ... tgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattctttatggctcacaatatttggatcattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
ggctcac putative branch site (score: 3)
tgtttttc putative PPT
acaatatttggatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaatctgttgacccattaaaagggtacggacttgttatagtaggattctttatggctcacaatatttggatcattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - tgaccca