Sequence
atgc intronic sequence ATGC exonic sequence...ctctagctgaatatctaggatttaaatttgtaagataagtctttcattatgactattaccctacttaggtagtaatgatatttactgatttgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
Basic information
species | Glycine max |
transcript | GLYMA08G18810.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G18810.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g14760.2 (Oryza sativa), 3'ss of exon 3
ctctagctgaatatctaggatttaaatttgtaagataagtctttcattatga--ctattaccctacttaggtagtaa-tgatatttac-tgatttgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
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----acttttttatctgttaatgatatcaggtaaacacctttctgtctatggatccaattgactattggatggataacttacactcatatttctttacctgtagGTGGTAGATTGCCGTATCTGTGGTGATCCACACTCAGTCTTGCGTTTTGCTTTCATTGAATTTGCTGATGATG
upper sequence: GLYMA08G18810.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G069816_T01 (Zea mays), 3'ss of exon 3
--ctctagctgaatatctaggatttaaatttgtaagataagtctttcattatgactattaccctacttaggtagtaatgatatttactgatttgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
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ctgtcaacatgatcttctattatatcaacatgatcttctattctgtcaacatgatcaatgatgttttttccta--aatcctaatgaacttcctctctcttagGTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG
upper sequence: GLYMA08G18810.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G051043_T01 (Zea mays), 3'ss of exon 3
----ctctagctga--atatctaggatttaaatttgt-aagataagtctttcattatgactattaccctacttaggtagtaatgatatttactgatttgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
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agtttattaagtgatcatgtttactggtctattctgtcaacatgaacaaatgaacaatggtgttttttt-cctaaatcataatgaactttc----tctctgtt--agGTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTCATTGAGTTCTCTGATGAAG
upper sequence: GLYMA08G18810.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G814159_T01 (Zea mays), 3'ss of exon 3
--ctctagctgaatatctaggatttaaatttgtaagataagtctttcattatgact-attaccctacttaggtagtaatgatatttactgatttgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
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cactgcagtttcaaaat--ggttcacaatgtgggcgatgt-tgtgtggttacattttatctttctatgtttgacttactacgacacatctttttcacatgtagGTGGTAGATTGCCGTATCTGTGGTGATCCTAACTCAGTGCTTCGTTTTGCTTTTATCGAGTTTGCTGATGACG
upper sequence: GLYMA08G18810.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G14450.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------ctctagctgaatatctaggatt----taaa---tttgtaagataagtctttcattatgactattaccctacttaggtagtaatgatatttactgatttgaat-tgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
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gtaagatgatccttaaaatctttaaatgttggttatatctttctatttcatgtgttttggacaatgtgttaaatttagactagtttttgagtccgtgccaaaggttctgttgaaaaaatgttactttggtggtatagttgtgtgtgtgaagtaacgttaagttcttcttcttttgtgaagGTTGTTGACTGTAGAATTTGTGGCGATCCACATTCGGTTCTTCGATTTGCGTTTGTTGAGTTTGCTGATGACC
upper sequence: GLYMA08G18810.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0176g00140.t01 (Vitis vinifera), 3'ss of exon 3
ctctagctgaatatc---taggatttaaatttg-taagataagtctttcattatgact-attaccctacttaggtagtaatgatatttactgatttgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
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---tagataggttttacacaaaattgagttttaacttgatagttggtttgttgtggttgatgagacta--tactttcttaagtttctggaatgcttattttgaagGTTGTTGATTGTCGAGTTTGTGGTGATCCGCATTCAGTTCTTCGTTTTGCATTTGTGGAGTTTGCTGATGAGCMapped 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|19934604|gb|BQ079634.1|BQ079634EST: GTTACTGAGGAGCGGCTTGCTGCCTTATTCAGCAGCTGTGGACAA GTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCT
genomic: GTTACTGAGGAGCGGCTTGCTGCCTTATTCAGCAGCTGTGGACAAgtaagttatg ... tgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgactattaccctacttaggtagtaatgatatttactgatttgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
tactgat putative branch site (score: 2)
tagtaatgatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctagctgaatatctaggatttaaatttgtaagataagtctttcattatgactattaccctacttaggtagtaatgatatttactgatttgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG