Sequence
atgc intronic sequence ATGC exonic sequence...gcatacttctaataaagctatttaatatggatgtttgtcaaaggcgtaatgtgaaaatttgtttaacacccggaataatatggtgtggtactctcttcagTTTGCAGGAGGCTTTGATGCAGAGAGCATGAAGGCTTTTGAAGACCTAAGGAACCGCATCCAAGCCTCTCAGGCTGGTGAAGATAACAAAACAGAAACAT
Basic information
species | Glycine max |
transcript | GLYMA02G11260.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G11260.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 5
------------------gcatacttctaataaagctatttaatatggatgtttgtcaaaggcgtaatgtgaaaatttgtttaacacccggaat----aatatggtgtggtactctcttcagTTTGCAGGAGGCTTTGATGCAGAGAGCATGAAGGCTTTTGAAGACCTAAGGAACCGCATCCAAGCCTCTCAGGCTGGT--GAAGATAACAAAACAGAAACAT
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gtgtgaggttctctttccgtgttcatcaggtaaaatcctcacgccaatattttcagaacccaggtacttcacaggtgatatgaatatttcgaatcagtaacttattcatctaccttctgcagTTTGCTGGGGGATTTGATGCAGAAAGCATGAAAGCTTTTGAAGAGCTAAGAAGCAAGATGAGTACACATAAATCTGCTCCACAGATATCTGAAGGCTGA---
upper sequence: GLYMA02G11260.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G25690.1 (Arabidopsis thaliana), 3'ss of exon 8
gcatacttctaataaagctatttaatatg-gatgtttgtcaaaggcgtaatgtgaaaatttgtttaacacccggaataatatggt-gtggtactctcttcagTTTGCAGGAGGCTTTGATGCAGAGAGCATGAAGGCTTTTGAAGACCTAAGGAACCGCATCCAAGCCTCTCAGGCTGGTGAAGATAACAA-AACAGAAACAT
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------gtaaaataaaaacaagaaacataagaaacctaaaatgaccaaaatttctcagttgtttgaatatataactgaatatgtttgttttgttatgtatagTTTGCTGGAGGGTTTGATGCAGAGAGCATGAAAGCATTTGAGGAACTTAGAAGCAGAGCCAAAACTGAAAGTGGAGACAATAATAATAATAATAATAATA-
upper sequence: GLYMA02G11260.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0011g02860.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------------------------------------------------------------------gcatacttctaataaagctatttaatatggatgtt--tgtcaaaggcgtaatgtgaaaatttgtttaacacccggaa-taatatggtg---tggtactctcttcagTTTGCAGGAGGCTTTGATGCAGAGAGCATGAAGGCTTTTGAAGACCTAAGGAACCGCATCCAAGCCTCTCAGGCTGGTGAAGATAACAAAACAGAAACAT---
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gtatgtttcgtttctgcatctgtttctgttaatttatacttcacatgttctacggtttacagaacaaatgatagaagtattttattttccctcaaattgggaagaacaaaacgtaaaatttgtagcaatgtgaataacaagaagttgaaaattgtgacaagtatggaaacaacattctgaattggacttgttcccagTTCGCGGGAGGCTTTGATGCGGAGAGCATGAAGGTTTTTGAAGAACTGAGGAGCCGTGTGAAAAC---ACAAACAGGCGAAGACAACAAGCTAGAAACATGAGMapped 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|10844840|gb|BF068041.1|BF068041EST: GAGAGTTTTTGGTTCTGCAAGGCGTGCGTTTCGCTTTCCGTGTCCATCAG TTTGCAGGAGGCTTTGATGCAGAGAGCATGAAGGCTTTTGAAGACCTAAGG
genomic: GAGAGTTTTTGGTTCTGCAAGGCGTGCGTTTCGCTTTCCGTGTCCATCAGgtaatgctag ... ctctcttcagTTTGCAGGAGGCTTTGATGCAGAGAGCATGAAGGCTTTTGAAGACCTAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaatgtgaaaatttgtttaacacccggaataatatggtgtggtactctcttcagTTTGCAGGAGGCTTTGATGCAGAGAGCATGAAGGCTTTTGAAGACCTAAGGAACCGCATCCAAGCCTCTCAGGCTGGTGAAGATAACAAAACAGAAACAT
gtttaac putative branch site (score: 3)
tactctcttc putative PPT
tgaaaatttgtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatacttctaataaagctatttaatatggatgtttgtcaaaggcgtaatgtgaaaatttgtttaacacccggaataatatggtgtggtactctcttcagTTTGCAGGAGGCTTTGATGCAGAGAGCATGAAGGCTTTTGAAGACCTAAGGAACCGCATCCAAGCCTCTCAGGCTGGTGAAGATAACAAAACAGAAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
gcatact
- - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtg