Sequence
atgc intronic sequence ATGC exonic sequencegtaggatgatgagtactatactatacaatacttcatgtttccatcatcactttatcaatatattgttgctgcagcatgtgcacaacacaacacaaaagtcatcatttgaattaattaaccttccttttttttaagatttaatttttttgtgttgtatatcttgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGATGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAGGAAGAGAACTCCAT
Basic information
species | Glycine max |
transcript | GLYMA19G41250.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G41250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 1
gtaggatgatgagtactatactatacaatacttcatgtttccatcatcactttatcaatatattgttgctgcagcatgtgcacaacacaacacaaaagtcatcatttgaattaattaaccttccttttttttaagatttaatttttttgtgttgtatatcttgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGATGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAGGAAGAGAACTCCAT
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-------------------------------------------gtacccatgtatgttcatctt-ttggtgtgtcac-tgta-aatgcagaacagcaaccgttattgagaccaagtctcctgtgttttttttt---tcttttttctctttctatcataattgg---cagGTTTGCAGAGGTGTGGGAAGAGCTGCAGGCTAAGATGGATTAACTACTTGAGGCCTGATTTGAAGAGGGGAGCATTCTCACAACAGGAAGAGAGCCTGAT
upper sequence: GLYMA19G41250.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaggatgatgagtactatactatacaatacttcatgtttccatcatcactttatcaatatattgttgctgcagcatgtgcacaacacaacacaaaagtc-atcatttgaattaattaaccttccttttttttaagatttaatttttttgtgttgtatatct--tgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGATGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAGGAAGAGAACTCCAT
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-----------------------------------------------------------------------cagaaagttttcttgattgccaatcagtttactatttttatacattgaatttaaaaaaact-aatgtctatttcgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
upper sequence: GLYMA19G41250.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S24_48V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaggatgatgagtactatactatacaatacttcatgtttccatcatcactttatcaatatattgttgctgcagcatgtgcacaacacaacacaaaagtcatcatttgaattaattaaccttccttttttttaagatttaatttttttgtgttgtatatcttg---tctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGATGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAGGAAGAGAACTCCAT
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--------------------------------------------------------------------tcgcttcatttgttcggaagaa-gttaaagttgctcctcgcatgg--caatagtgttggattgggtgatctagctcttacac-ttgtgtgctacggaacaacagGATTACAGCGATGTGGGAAGAGCTGCAGGTTAAGGTGGATAAATTATCTGAGGCCCGACTTAAAGCGAGGTGTCTTCTCTCCAGCGGAGGAGAATCTGATMapped 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|6341619|gb|AW164443.1|AW164443EST: CATCACCAAACATGGCCATGGATGTTGGAGCTCCGTTCCAAAACTAGCTG GTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGATGGATAAATTATCTCA
genomic: CATCACCAAACATGGCCATGGATGTTGGAGCTCCGTTCCAAAACTAGCTGgtaggatgat ... cttgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGATGGATAAATTATCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaccttccttttttttaagatttaatttttttgtgttgtatatcttgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGATGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAGGAAGAGAACTCCAT
atttaat putative branch site (score: 4)
tcttgtctc putative PPT
ttttttttaagattta 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
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gtaggatgatgagtactatactatacaatacttcatgtttccatcatcactttatcaatatattgttgctgcagcatgtgcacaacacaacacaaaagtcatcatttgaattaattaaccttccttttttttaagatttaatttttttgtgttgtatatcttgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGATGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAGGAAGAGAACTCCAT
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