Sequence
atgc intronic sequence ATGC exonic sequence...ttaattaaggtatagccaaaatccaaatgttcccttagttatgaacttatgatttgtttaatgtatcctgattttccttcattaaggttgtcttttgcagATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGACAAAGGAAACTGTGTGGGGATTGCATTTCAGTCCCTCAAGCATGAAGATG
Basic information
species | Glycine max |
transcript | GLYMA05G01930.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G01930.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------ttaattaaggtatagccaaaatccaaatgttcccttagttatgaacttatgatttgtttaatgtatcctgat-tttccttcattaaggttgtcttttgcagATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGACAAAGGAAACTGTGTGGGGATTGCATTTCAGTCCCTCAAGCATGAAGATG
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gtttttctcttaagatctttgcatgcttttgattgtctatattttgcatattgtagacatagtttttacttctctttggaattatttctaataatctcttaacctgggagcatacttaagttttcactgtttcatggaacagATAGATGCAGCTATAAATTCAGGAAACTCTGGGGGCCCTGCTTTTAATGATAAGGGCAAGTGTGTGGGCATAGCTTTTCAATCTCTTAAACACGAAGATG
upper sequence: GLYMA05G01930.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
-ttaattaaggtatagccaaaatccaaatgttcccttagttatgaacttatgatttgtttaatgtatcctgattttccttcattaaggttgtcttttgcagATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGACAAAGGAAACTGTGTGGGGATTGCATTTCAGTCCCTCAAGCATGAAGATG
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gttggacaa--cacatttgacatg-atatttttccttatct---gactaggga---gttaagggcacttataaaaatgttttctgtttttgtctttt-cagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
upper sequence: GLYMA05G01930.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 2
ttaattaaggtatagccaaaatccaaatgttcccttagttatgaacttatgatttgtttaatgtatcctgattttccttcattaaggttgtcttttgcagATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGACAAAGGAAACTGTGTGGGGATTGCATTTCAGTCCCTCAAGCATGAAGATG
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---gtcatggggtcacatttctcctttttctcttttagttattgttggcttgttgatccattt--ttctgatgtctcctattcttgatggt--tttacagATAGATGCTGCTATAAACTCTGGAAATTCTGGTGGGCCTGCCTTCAATGAGAAGGGCAATTGTGTGGGCATTGCATTTCAGTCTCTTAAACATGAAGATGMapped 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|7285317|gb|AW597804.1|AW597804EST: TTGAGATTCTATCTTATGTCCATGGTTCTACAGAACTTCTAGGTTTACAG ATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGAC
genomic: TTGAGATTCTATCTTATGTCCATGGTTCTACAGAACTTCTAGGTTTACAGgttaggttga ... tcttttgcagATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGAC
EST:
gi|7284465|gb|AW597055.1|AW597055EST: TTGAGATTCTATCTTATGTCCATGGTTCTACAGAACTTCTAGGTTTACAG ATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGAC
genomic: TTGAGATTCTATCTTATGTCCATGGTTCTACAGAACTTCTAGGTTTACAGgttaggttga ... tcttttgcagATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatgatttgtttaatgtatcctgattttccttcattaaggttgtcttttgcagATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGACAAAGGAAACTGTGTGGGGATTGCATTTCAGTCCCTCAAGCATGAAGATG
tcctgat putative branch site (score: 3)
ttgtctttt putative PPT
atttgtttaatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaattaaggtatagccaaaatccaaatgttcccttagttatgaacttatgatttgtttaatgtatcctgattttccttcattaaggttgtcttttgcagATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGACAAAGGAAACTGTGTGGGGATTGCATTTCAGTCCCTCAAGCATGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - atccaaa
- - - - - - - - - - - - - -tgttccc
- - - - - - - - - - - - - - - - - - - -tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - -tgatttg