Sequence
atgc intronic sequence ATGC exonic sequencegttagtacctctaaagtatatattggcaatgtcaatttggcaaatttcaattttgttttccgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
Basic information
species | Glycine max |
transcript | GLYMA07G01890.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 13
--------gttagtacctctaaagtatatat---tggcaatgtcaatttggcaaatttcaattttgttttccgctgactatgatcttggactc----cagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
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gagaagccattcacagcgcaaacacttgggtgtcttgtaatgtttactgttggtatttattatgagcaagaagccaagaactgacttgaatgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGC
upper sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
--------gttagtacctctaaagtatatattggcaatgtcaatttggcaaatttcaat---tttgttttccgctgactatgatcttggactc----cagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
|| |||| | ||||| | | | || | || | | | | | | | | | | || | || | |||| || || ||| || ||||| || ||||| || ||||||||||| ||||||||||| ||||| ||||||| |||||| || || || ||| | |||||
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
upper sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
-----gttagtacctctaaagtata--tattggcaatgtcaatttggcaaatttcaattttg--ttttccgctgacta----tgatcttggact--ccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
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gtcaagctgcgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
upper sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
---------gttagt--acctctaaagtatatattggcaatgtcaatttggcaaat--ttcaattttgttttccgctgactatgatct--tggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
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ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
upper sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
gttagtacctctaaagtatatattggcaatgtcaatttggcaaatttcaattttgttttc---------------cgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
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ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
upper sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
------------------------------------------------------------------------gttagtacctctaaagtatatattggcaatgtcaatttgg----caaatttcaattttgttttccgc-tgac----tatgatcttggactcc--agGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
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gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
upper sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gttagtacctctaaagtatatattggcaatgtcaatttggcaaatttcaattttgttttccgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
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-------------------------gtattgtcgctgttattgatggccactggcattgtcgctgac-gcgtgtttcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC
upper sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gttagtacctctaaagtatatattggcaatgtcaatttggcaaatttcaattttgttttccgctgac-tatgatcttggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
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-------------------gtattgtcgctgtta--ttgatggccactggcattgtt----gctgacgcgtgattccc--ccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGCMapped 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|22930150|gb|BU547289.1|BU547289EST: AGCTGTAAACGGGAGCTCGCTAGTAGTAATGTCTAAGG GCACACAGTATTTGCAACAATCATATAAAGTTAGTGACTCATTTCCTTTCA
genomic: AGCTGTAAACGGGAGCTCGCTAGTAGTAATGTCTAAGGgttagtacct ... tggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcaatttggcaaatttcaattttgttttccgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
cgctgac putative branch site (score: 3)
aaatttcaattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtacctctaaagtatatattggcaatgtcaatttggcaaatttcaattttgttttccgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG