Sequence
atgc intronic sequence ATGC exonic sequencegtaggatgatgagtactatacaacactttatcaatattaatattgcatcatgtttgtccacaacacaacacaaaagtcattttacttaattaaccttccttctctcaaactttgtgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAAGAAGAGAATTCCAT
Basic information
species | Glycine max |
transcript | GLYMA03G38660.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G38660.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 1
gtaggatgatgagtact-atacaacactttatcaatattaatattgcatcatgtttgtccacaacac-aacacaaaagtcattttacttaattaaccttccttctctcaaactttgtgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAAGAAGAGAATTCCAT
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--gtacccatgtatgttcatcttttggtgtgtcactgtaaatgcagaacagcaaccgttattgagaccaagtctcctgtgttttttttttcttttttctctttctatcataattgg-----cagGTTTGCAGAGGTGTGGGAAGAGCTGCAGGCTAAGATGGATTAACTACTTGAGGCCTGATTTGAAGAGGGGAGCATTCTCACAACAGGAAGAGAGCCTGAT
upper sequence: GLYMA03G38660.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaggatgatgagtactatacaacactttatcaatattaatattgcatcatgtttgtccacaacacaacacaaaagtcattttacttaattaaccttccttctctcaaactttgtgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAAGAAGAGAATTCCAT
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------------------cagaaagttttcttgattgccaatcagtttactatttttatacattg-aatttaaaaaaactaatgtctattt---cgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
upper sequence: GLYMA03G38660.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaggatgatgagtactatacaacactttatcaatattaatattgcatcatgt--ttgtccacaacacaacacaaaagtcattttacttaattaaccttccttctctcaaactttgtgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAAGAAGAGAATTCCAT
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--------------tttcctctttgctctaaaaaaagaaaagttcagataccccgttgacaccaatttagaataagagttgtgtcgctgac---gctggtgtgccctggaacaa-------cagGGTTACAGAGATGTGGAAAAAGCTGCAGGTTAAGGTGGATAAACTATCTGAGGCCAGACTTAAAGCGAGGGGTTTTCTCACCAGCAGAGGAGAATCTGAT
upper sequence: GLYMA03G38660.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S24_48V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaggatgatgagtactatacaacactttatcaatattaatattgcatcatgtttgtccacaacacaacacaaaagtcattttacttaat-taaccttccttctctcaaactttgtgtct-cagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAAGAAGAGAATTCCAT
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----------------------tcgcttcatt--tgttcggaagaagttaaagttgctcctcgcatggcaatagtgttggattgggtgatctagctcttacacttgtgtgctacggaacaacagGATTACAGCGATGTGGGAAGAGCTGCAGGTTAAGGTGGATAAATTATCTGAGGCCCGACTTAAAGCGAGGTGTCTTCTCTCCAGCGGAGGAGAATCTGATMapped 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|22522173|gb|BU080984.1|BU080984EST: CATCACCAAACATGGCCATGGATGTTGGAGCTCCGTTCCAAAACTAGCTG GTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCA
genomic: CATCACCAAACATGGCCATGGATGTTGGAGCTCCGTTCCAAAACTAGCTGgtaggatgat ... tgtgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacaaaagtcattttacttaattaaccttccttctctcaaactttgtgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAAGAAGAGAATTCCAT
aattaac putative branch site (score: 2)
aaagtcattttactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggatgatgagtactatacaacactttatcaatattaatattgcatcatgtttgtccacaacacaacacaaaagtcattttacttaattaaccttccttctctcaaactttgtgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAAGAAGAGAATTCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA