Sequence
atgc intronic sequence ATGC exonic sequence...aacaacaccgaaaatatctaatgaattgtatccaagttttgtcctttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaatgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG
Basic information
species | Glycine max |
transcript | GLYMA19G27570.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G27570.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g36420.1 (Oryza sativa), 3'ss of exon 2
aacaacaccgaaaatatctaatgaattgtatccaagttttgtcctttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaatgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG
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tgcagcattttcctttgatcagcagtagaagtttcatttacatgttctttactctcttgcttcttttctagcttgcttctgaaatctcaactttatttagGCAAGAAGGGGACTTGGCCTCACAGCAGATATTATTGATCATTGCAAGCTAGTCCTTAGATTTCCTAAAGGAACCAACAGCACTTGG
upper sequence: GLYMA19G27570.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G119791_T05 (Zea mays), 3'ss of exon 2
-----aacaacaccgaaaatatctaatgaattgtatccaagttttgtcctttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaatgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG-------------
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tatgcaacatttcctcagcctggcagtgcaaagcttgcttgcttatttttcttctgttgtttgatcatcttc-----tatcttctgaaatctcgtctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGGTCAGTATTCCTC
upper sequence: GLYMA19G27570.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G119791_T03 (Zea mays), 3'ss of exon 2
-----aacaacaccgaaaatatctaatgaattgtatccaagttttgtcctttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaatgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG
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tatgcaacatttcctcagcctggcagtgcaaagcttgcttgcttatttttcttctgttgtttgatcatcttc-----tatcttctgaaatctcgtctttatttagGCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG
upper sequence: GLYMA19G27570.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G136098_T01 (Zea mays), 3'ss of exon 2
aacaacaccgaaaatatctaatgaattgtatccaagtt--ttgtcctttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaatgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG
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gactatatgcaacatttcc--tcagcagtgctaagcttgcttgcttatttttcttctgttgtttgatcatcttctatcttctgaaatctcgtctttatttagGCTAGCAGAGGACTTGGTCTCACAACACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCAGG
upper sequence: GLYMA19G27570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g01150.t01 (Vitis vinifera), 3'ss of exon 2
aacaacaccgaaaatatctaatg--aattgtatccaagttttgtcctttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaa-tgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG
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tgagactctgtgaatatagggtttcagtttatttgttgaagtgcactttctag---ttagtctttggttcatattgtgggctaaacttggaaactttgtgcagGCAAACAGAGGGTTTGGAATTACTGCACATATTATTGACCACTGCAAATTGATTCTCAAGTTCCCTGAAGGCACTAACAGTACCTGGMapped 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|209714617|gb|BW654130.1|BW654130EST: AGACAATCCGCGTTTTGTCTAACGTTCAGTCCAGTGTGAAGCAATGTGTG GATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTA
genomic: AGACAATCCGCGTTTTGTCTAACGTTCAGTCCAGTGTGAAGCAATGTGTGgtaactcttc ... atgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaatgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG
ttttaac putative branch site (score: 2)
ttttaaaaaaaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacaacaccgaaaatatctaatgaattgtatccaagttttgtcctttttaacttttaaaaaaaaataaaaaatagaatctgaggttgggaatgaaaacagGATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- caacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttggg