Sequence
atgc intronic sequence ATGC exonic sequence...tcatagttttgttgtgcatactatgtctttaacatatatgatatgcataacatagtttagcaactcctccagttctaaatcttgttgaatgaaaatgcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGATTCAGGATTCAACATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCA
Basic information
species | Glycine max |
transcript | GLYMA16G26940.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
tcatagttttgttgtgcatactatgtctttaacatatatgatatgcataacatagtttagcaactcctccagttctaaatcttgttgaatgaaaatgcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGATTCAGGATTCAACATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCA
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acttaaccaggatcagtattttataaggttcatctgggctttcccccctatccgaaacagtatgttcaacttttgagtaacaagcagtttgtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 1
--tcatagttttgttgtgcatactatgtctttaacatatatgatatgcataacatagtttagcaactcctccagttctaaatcttgttgaatgaaaat-gcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGATTCAGGATTCAACATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCA
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gttcgatgttttcctctgttttct---tcttccatctataacagatctgcagaaccgatc--cggttcaagatcatttgaacggaactaaccaactattgcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 3
tcatagttttgttgtgcatactatgtctttaacatatatgata--tgcataacata--gtttagcaactcctccagttctaaatcttgttgaatgaaaatgcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGATTCAGGATTCAACATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCA
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--gtggtttctaatgatatgctcagttttct-catccatgataaccgtatgatttaccattttttgactatgctcttttcacttctt-ttgaacaaaattgcagGTTGAGTGCACCATACCCAAAGACGATGGTACTTTGGCATCATTTGTTGGATTCAGGGTTCAACATGACAATGCTAGAGGCCCCATGAAGGGAGGGATCAMapped 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|254319541|gb|GR829053.1|GR829053EST: TGGATTCCAAGCTTGAGAAAAGTTTGCTGATTCCATTTAGAGAAATCAAG GTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGA
genomic: TGGATTCCAAGCTTGAGAAAAGTTTGCTGATTCCATTTAGAGAAATCAAGgcaagtaaac ... gaaaatgcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGA
EST:
gi|23731633|gb|BU763952.1|BU763952EST: TGGATTCCAAGCTTGAGAAAAGTTTGCTGATTCCATTTAGAGAAATCAAG GTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGA
genomic: TGGATTCCAAGCTTGAGAAAAGTTTGCTGATTCCATTTAGAGAAATCAAGgcaagtaaac ... gaaaatgcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cataacatagtttagcaactcctccagttctaaatcttgttgaatgaaaatgcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGATTCAGGATTCAACATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCA
ttctaaa putative branch site (score: 2)
aatgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatagttttgttgtgcatactatgtctttaacatatatgatatgcataacatagtttagcaactcctccagttctaaatcttgttgaatgaaaatgcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGATTCAGGATTCAACATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - -gcatact
- - - - - - - - - - - - - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgttg