Sequence
atgc intronic sequence ATGC exonic sequencegtaaataacatttatgggactgctttttcatctacaatttaagctagaggttcatcaatttgatagttttcctggacatgggatgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA
Basic information
species | Glycine max |
transcript | GLYMA05G32070.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 11
gtaaataacatttatgggactgctttttcatctacaatttaagctagaggttcatcaatttgatagttttcctggacatgggatgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA
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----gtaaatttttccaacctaaaaatgtggttat--tccaatctatatatacttcgctgaaatgcgatgcaatgatctt---ttcagGCTCAGCAATTGAACAAGGATATTTTTGAGACTATTTATTATCATGCCTTGAAAGCTTCTGCTGAAATTGCTGCAAAAGAAGGTCCTTATGAAACTTATA
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 11
gtaaataacatttatgggactgctttttcatctacaatttaagctagaggttcatcaatttgatagttttcctggacatggga-------tgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA
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----gtaacttttcctagttcagtaatatagtagtactagttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTGAAAGCTTCCGCTGAGCTTGCTGGTAAAGAAGGTCCCTATGAAACATATG
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 11
gtaaata---acatttatgggactgctttttcatctacaatttaagctagaggttcatcaatttg-atagttttcctggacatgggatgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA
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gtacctttccatttctatgtagctcatcattaaccatatgttcctttctgtaattagttgatatgtaacaaatggttttatatt---ttcagGCTCATCAGTTGAATAAGGATATATTTGAAACTATCTACTATCATGCTCTGAAATCTTCTGCTGAACTTGCTGTTAAAGAAGGTCCCTATGAAACATATG
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 11
---gtaaataacatttatgggactgctttttcatctacaatttaagctagaggttcatcaatttg--atagttttcctggacatgggatgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA
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gtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatctt----ttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 11
gtaaa-taacatttatgggactgctttttcat----ctacaatttaagctagaggttcatcaatttgatagttttcctggacatgggatgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA
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gtaaagctaattttgcagggcaaatacttcattgtgctcctgtggattccaatgatacttagctgtgataattaatttgactattgactgcagGCTCAACAGCTTAACAAAGACATATTTGAGACCATATACTACCATGCTCTAAAGGCTTCTTGTGAGTTGGCTATGAGAGAAGGCCCCTATGAGACTTATGMapped 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|192296534|gb|FG991640.1|FG991640EST: GTCTTGCCGATACCTTCATACTACTAGGTGTGGCATTTGATTCACCAGAG GCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTA
genomic: GTCTTGCCGATACCTTCATACTACTAGGTGTGGCATTTGATTCACCAGAGgtaaataaca ... tgggatgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTA
EST:
gi|19345937|gb|BM890817.1|BM890817EST: GTCTTGCCGATACCTTCATACTACTAGGTGTGGCATTTGATTCACCAGAG GCTCAGCAGTTGAAACA-GGATATATTTGAGACTATATACTATCATGCACT
genomic: GTCTTGCCGATACCTTCATACTACTAGGTGTGGCATTTGATTCACCAGAGgtaaataaca ... tgggatgcagGCTCAGCAGTTGAA-CAAGGATATATTTGAGACTATATACTATCATGCACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaatttaagctagaggttcatcaatttgatagttttcctggacatgggatgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA
atttgat putative branch site (score: 5)
aatttgatagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataacatttatgggactgctttttcatctacaatttaagctagaggttcatcaatttgatagttttcctggacatgggatgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG