Sequence
atgc intronic sequence ATGC exonic sequencegtatagttttagttatgtagttatatatctcacacaaagccctcttttttaacgtacagttattacttttgacttttgtgcttctattctatgtatggttgttttatatattttttgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCTTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
Basic information
species | Glycine max |
transcript | GLYMA20G22230.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G22230.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 2
gtatagttttagttatgtagttatatatctcacacaaagccctcttttttaacgtacagttattacttttgacttttgtgcttctattctatgtatggttgttttatatattttttgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCTTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
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----------------gtactt-taaatcctgtcagcaacctcctacaagaacccacttttaata-tagtagttttcctg-ttggattct-------gaagtttt------ctgctgtttcatcagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
upper sequence: GLYMA20G22230.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 2
gtatagttttagttatgtagttatatatctcacacaaagccctcttttttaacgtacagttattacttttgacttttgtgcttctattctatgtatggttgttttatatattttttgctttat---cagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCTTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
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------------------------ctgagacacgataaggtcacatgttggtaata-agctatcccccccccccccc---cccccctgcta-gttgggctaatgcagcaattgatccccttgcatgcagGTGGTCTCAGATTGCAACTCAGTTACCAGGCCGCACCGACAACGAAATCAAAAACTTCTGGAACTCCTGTATCAAGAAGAAGCTTCGCAACATCGGCATCMapped 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|7589095|gb|AW704876.1|AW704876EST: CAACAGGAAGAAAACATGATTGTTGAACTTCATGCAGTTCTTGGAAACAG GTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAA
genomic: CAACAGGAAGAAAACATGATTGTTGAACTTCATGCAGTTCTTGGAAACAGgtatagtttt ... gctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttgtgcttctattctatgtatggttgttttatatattttttgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCTTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
ttttgac putative branch site (score: 3)
ttttttgctttatc putative PPT
tatgtatggttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagttttagttatgtagttatatatctcacacaaagccctcttttttaacgtacagttattacttttgacttttgtgcttctattctatgtatggttgttttatatattttttgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCTTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
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