Sequence
atgc intronic sequence ATGC exonic sequencegtagattatttataagcaattcaaatgtttcatggctccttgtaagtttcttttcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
Basic information
species | Glycine max |
transcript | GLYMA04G39500.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 5
gtagattatttataagcaattcaaatgtttcatggctccttgtaagtttcttttcttacctgtatgtatgattatgctcttctt----ttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
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gtaggtt--ctatggtcaattttatt-tgtgaaaattactc-taa-----taccataatctccaggaattctcataccctcctaaaaatcagGTGCATTTGCTGTGTACTTGGAGCCTTGGCATGCGGATATTTTTGAGTTCCTTGATCTGAGAAAGAATCATGGGAAG
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 5
gtagattatttataagcaattcaaatgtttcatggctccttgtaagtttc-ttttcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
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gtaaata--ccatcagttagttagacatggacctaat--ttacatgttcagtgttcaggatttcttatggattcctaacattaatttagGTGCATTTGCTATATACTTGGAGCCTTGGCATGCTGATATTTTTGAGTTCCTTGATTTAAGAAAGAACCATGGAAAG
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 5
gtagattatttataagcaattcaaatgtttcatggctccttgtaagtttcttttctt-acctgtatgtatgattatgctcttct-----tttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
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----------------------gtatgtttcttcattatcgtcgcttttagttccttcatcttcagaaattctaacgagcttctaaaaacttagGTGCATTTGCTGTATACTTGGAGCCTTGGCATGCTGATATTTTTGAGTTCCTTGATCTGAGAAAGAACCATGGGAAG
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 5
gtagattatttataagcaattcaaatgtttcatggctccttgtaagtttcttttcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
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---------gtatgctttttttcattatttcc--acttttagtaacatcgtcttcagaaattcttatgagcttctaaaact----tagGTGCATTTGCTGTATACTTGGAGCCTTGGCATGCTGATATTTTCGAGTTCCTTGATCTAAGAAAGAACCATGGGAAG
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 5
gta-gattatttataagcaattcaaatgtttcatggctccttgtaagtttcttttcttacct---gtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
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gtacaatcattaaaccttgctttattttgctgagggtaatgttcaaaaatttgattgtgccttgtgtaaatgtgataat-ctctgcatacagGTGCTTTTGCTGTGTACTTGGAGCCATGGCATGCTGACATATTTGAGTTTCTAGATCTTAGGAAAAACCATGGAAAGMapped 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|193362309|gb|FK325259.1|FK325259EST: GTTCAATGATACTGCCCGCTATGTTGATCAGGGGGGAGGCAAAAGGAAAG GTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCT
genomic: GTTCAATGATACTGCCCGCTATGTTGATCAGGGGGGAGGCAAGAGGAAAGgtagattatt ... cttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCT
EST:
gi|208182565|gb|GD980788.1|GD980788EST: GTTCAATGATACTGCCCGCTATGTTGATCAGGGGGGAGGCAAGAGGAAAG GTGCATTTGCTGTGTA
genomic: GTTCAATGATACTGCCCGCTATGTTGATCAGGGGGGAGGCAAGAGGAAAGgtagattatt ... cttcttttagGTGCATTTGCTGTGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctccttgtaagtttcttttcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
ttcttac putative branch site (score: 2)
ttatgctcttctttt putative PPT
tatgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagattatttataagcaattcaaatgtttcatggctccttgtaagtttcttttcttacctgtatgtatgattatgctcttcttttagGTGCATTTGCTGTGTACTTGGAGCCATGGCATGCTGATATGTTTGAATTCTTGGATTTAAGGAAAAATCATGGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA