Sequence
atgc intronic sequence ATGC exonic sequence...gaaatttcatgtgtcacaatgtagtttatctgcaaatgtttacataatgaagaatctggtaaaaaccttatgattgaagttccttaatgttatcatgtagGGAACTTCAGATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAACTGTGTAAAGAGAAGTATGAGCCACTATGGCTCAAAGGAGGAAACCACT
Basic information
species | Glycine max |
transcript | GLYMA05G24080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G24080.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G039214_T01 (Zea mays), 3'ss of exon 4
gaaatttcatgtgtcacaatgtagtttatctgcaaatgtttacataatgaagaatctggtaaaaaccttatgattgaagttcct---taatgttatcatgtagGGAACTTCAGATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAACTGTGTAAAGAGAAGTATGAGCCACTATGGCTCAAAGGAGGAAACCACT
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---tttttttacattaacttgaacatttcttggtttaatttgctcaaatctatgcatgctatttgattcattactggtgctcatagctcttgctgaaatgtagGGAACTGCTGATGAAGTGGTGGATTGGTCTCATGGTAAACAACTTTGGGAACTTTGCAAAGACAAGTATGAGCCCTTATGGCTCAGGGGAGGAAAGCACT
upper sequence: GLYMA05G24080.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G14390.1 (Arabidopsis thaliana), 3'ss of exon 4
-gaaatttcatgtgtcacaatgtagtttatctgcaaatgtttacataatgaagaatctggtaaaaaccttatgattgaagttccttaatgttatcatgtagGGAACTTCAGATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAACTGTGTAAAGAGAAGTATGAGCCACTATGGCTCAAAGGAGGAAACCACT
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gtgagttccatat---tcattttactctcttttcctttttttcagt--tcgaaaactgagtgtatataac-tctttgtggttcttc--tcttgtg--gcagGGAACTTGTGATGAAGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAACTCTCTAAAGAGAAATATGAACCGCTTTGGCTCGAAGGCGGTAACCACT
upper sequence: GLYMA05G24080.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0219g00290.t01 (Vitis vinifera), 3'ss of exon 4
-----gaaatttcatgtgtcacaatgtagtttatctgcaaatgtttacataatgaagaatctggtaaaaaccttatgattgaagttccttaatgt--tatcatgtagGGAACTTCAGATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAACTGTGTAAAGAGAAGTATGAGCCACTATGGCTCAAAGGAGGAAACCACT
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ttatgagagctacatctattaacataaagtt-----gggactatct-ca-gatgttatttttatttaaacctcttttattttgattattttatatctttttgtgtagGGAACTTCAGATGAAGTAGTTGATTGTTCCCATGGCAAGCAACTCTGGGAACTGTGTAAAGAGAAGTATGAACCTCTATGGCTTAAAGGAGGGAACCACTMapped 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|26056221|gb|CA799135.1|CA799135EST: AATATCGACAAAATTCCACTCGTTAATTGCCCTATTCTCATAATTC-- ---A--T---ATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAA
genomic: AATATCGACAAAATTCCACTCGTTAATTGCCCTATTCTCATAATTCATgtaagttttc ... tatcatgtagGGAACTTCAGATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgaagaatctggtaaaaaccttatgattgaagttccttaatgttatcatgtagGGAACTTCAGATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAACTGTGTAAAGAGAAGTATGAGCCACTATGGCTCAAAGGAGGAAACCACT
ccttaat putative branch site (score: 4)
ttaatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaatttcatgtgtcacaatgtagtttatctgcaaatgtttacataatgaagaatctggtaaaaaccttatgattgaagttccttaatgttatcatgtagGGAACTTCAGATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAACTGTGTAAAGAGAAGTATGAGCCACTATGGCTCAAAGGAGGAAACCACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - tcatgtg
- - - - - - - - -aatgtag
- - - - - - - - - - - - - -atctgca
- - - - - - - - - - - - - - - - - - - - - - -aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttatg