Sequence
atgc intronic sequence ATGC exonic sequence...atgtgtgcatttggatgttttcatctgcagaaacattatgaaagcttgaacccaactgactgattcagtttttttaccttctctctaaatgttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCAATGTCCATGAGATCTGGTGTAGCTGCTGATGCTGCAGCTGCATTGCTTT
Basic information
species | Glycine max |
transcript | GLYMA09G07240.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g08700.8 (Oryza sativa), 3'ss of exon 10
--------------------------------atg-tgtgcatttggatgttttcatctgcagaaacattatgaaagcttg--aacccaactgactgattcagtttttttaccttctctctaaatgttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCAATGTCCATGAGATCTGGTGTAGCTGCTGATGCTGCAGCTGCATTGCTTT
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gtatatcatacatctctctggctgttgtttcagtgctatcaatcaagatgacacatcatgcaatattatcataacagcacattatgtgttttgaatatttta--ttgattgtcatagctttgttttatgttttagCTTCCAAAGAACTGGATGCATCTTCATTTCCTGCGTGCTATTGGAACTGCAATGTCAATGAGAGCTGGTATCGCTGCTGATACGTCTGCTGCTTTACTTT
upper sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G107101_T06 (Zea mays), 3'ss of exon 9
atgtgt-gcatttggatgttttcatctgcagaaacattatgaaagct-tga-acccaactgactgattcagttttt---ttaccttctctctaaatg-----------ttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCAATGTCCATGAGATCTGGTGTAGCTGCTGATGCTGCAGCTGCATTGCTTT
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gtatgccatacttcacagattatccttgcaaaattgtcaagttgcctatgatacaaaattgtctaaccacatctttggttcaactttttgttaactgtggcactttattttttgtagCTTCCAAAAAATTGGATGCATCTGCATTTCTTGCGTGCGATTGGAACTGCAATGTCAATGAGAGCTGGCATTGCTGCTGATACAGCTGCTGCTTTGCTTT
upper sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 9
--atg-tgtgcatt-tggatgttttcatctgcagaaacattatgaaagcttgaacccaa------ctgactgattcagtttttttaccttctctctaaatgttaa--------------tacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCAATGTCCATGAGATCTGGTGTAGCTGCTGATGCTGCAGCTGCATTGCTTT
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gtatgacatacttcacagattattttgagtgcaaaattatcaagttgcctacgatacaaaattgtccggccacatttgtgtgtgtaaattttcattaactgtgatacttttattttatttgtagCTTCCAAAGAATTGGATGCATCTGCATTTCTTGCGTGCCATTGGAACTGCAATGTCAATGAGAGCTGGTATTGCTGCTGATACAGCTGCTGCTCTGCTTT
upper sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------atgtgtgcatttggatgttttcatctgcagaaacattatgaaagcttgaacccaactgactgattcagttttt-ttaccttctctctaaatgttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCAATGTCCATGAGATCTGGTGTAGCTGCTGATGCTGCAGCTGCATTGCTTT
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gtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagctttggtatgtcatcaaagaaatcagctttgatcacattctttttc----ttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
upper sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 10
atgtgtgcatttggatgttttcatctg-cagaaacattatgaaagct-tgaacccaactgactgattcagtttttttacct---tctctctaaatgttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCAATGTCCATGAGATCTGGTGTAGCTGCTGATGCTGCAGCTGCATTGCTTT
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--gaatgaaattgtggatttagaacagatttagacattgttcaactaatgaattcagttgtca---tcaatgctcatatctaaattgcttttcttattgatatagCTCCCAAGGAACTGGATGCATTTGCATTTCTTGCGTGCAATTGGTACTGCAATGTCCATGAGAGCAGGGATTGCTGCAGATGCTGCTGCAGCATTACTTTMapped 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|120531323|gb|EH259456.1|EH259456EST: AGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGG CTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCA
genomic: AGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGGgtaagctgta ... gttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaacccaactgactgattcagtttttttaccttctctctaaatgttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCAATGTCCATGAGATCTGGTGTAGCTGCTGATGCTGCAGCTGCATTGCTTT
attcagttttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtgtgcatttggatgttttcatctgcagaaacattatgaaagcttgaacccaactgactgattcagtttttttaccttctctctaaatgttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCAATGTCCATGAGATCTGGTGTAGCTGCTGATGCTGCAGCTGCATTGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - -tgcattt
- - - - - - ggatgtt
- - - - - - - - - - -catctgc
- - - - - - - - - - - - - - - - - - - - - -gcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - cccaact