Sequence
atgc intronic sequence ATGC exonic sequencegtattattattactcttcttctcctttctttttatttggattattattattaagtgggttttttcttcttaattatttacagGCCATTGATGATGATTGCAATCAAACTGGGCAGATGATAGCAGGACTCCTCAACTGGCCTCAAGGGACTTTTGCTTCTAAG
Basic information
species | Glycine max |
transcript | GLYMA20G34520.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34520.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G173040_T02 (Zea mays), 3'ss of exon 1
---------gtattattattactcttcttctcctttctttttatttggattattattattaagtgggttttttctt---------cttaattatttacagGCCATTGATGATGATTGCAATCAAACTGGGCAGATGATAGCAGGACTCCTCAACTGGCCTCAAGGGACTTTTGCTTCTAAG
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gatataaccctcctctagtcaagactcaccaagtttaacttacttgggagtatatctgctgagaatctatgttcctgagtccttgtcttgtcactaacagGCAATTGATGATGATTGCAACCAAACTGGACAAATGTTAGCTGGATTGCTCAAGTGGCCACAAGGAACCTTTGCCTCCAAG
upper sequence: GLYMA20G34520.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0049g00470.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------gtattattattactcttcttctcctttctttttatttggattattattattaagtgggttttttcttcttaatta----------tttacagGCCATTGATGATGATTGCAATCAAACTGGGCAGATGATAGCAGGACTCCTCAACTGGCCTCAAGGGACTTTTGCTTCTAAG
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gtctgtgaattcgtgcccagagattagggtttttggtaacgatttaaaaataaatttgcggattccgtgaaaat-cctagactctttttat--ggtggattgttgttttctgatgtgggcatgggttttctagGCCATTGATGACGATTGCAATCAAACAGGGCAAATGGTTGCCGGGTTGCTCAACTGGCCTCAGGGGACCTTTGCTTCCAAGMapped 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|14259523|gb|BG882431.1|BG882431EST: GAAAACTCGTCGAGATTGAGAAACCCGCTCTTCTCATCCTTGGCAAACAG GCCATTGATGATGATTGCAATCAAACTGGGCAGATGATAGCAGGACTCCTC
genomic: GAAAACTCGTCGAGATTGAGAAACCCGCTCTTCTCATCCTTGGCAAACAGgtattattat ... ttatttacagGCCATTGATGATGATTGCAATCAAACTGGGCAGATGATAGCAGGACTCCTC
EST:
gi|17401818|gb|BM178600.1|BM178600EST: GAAAACTCGTCGAGATTGAGAAACCCGCTCTTCTCATCCTTGGCAAACAG GCCATTGATGATGATTGCAATCAAACTGGGCAGATGATAGCAGGACTCCTC
genomic: GAAAACTCGTCGAGATTGAGAAACCCGCTCTTCTCATCCTTGGCAAACAGgtattattat ... ttatttacagGCCATTGATGATGATTGCAATCAAACTGGGCAGATGATAGCAGGACTCCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttatttggattattattattaagtgggttttttcttcttaattatttacagGCCATTGATGATGATTGCAATCAAACTGGGCAGATGATAGCAGGACTCCTCAACTGGCCTCAAGGGACTTTTGCTTCTAAG
tcttaat putative branch site (score: 3)
ttttttcttcttaatt CT-rich tract
tatttggattattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattattattactcttcttctcctttctttttatttggattattattattaagtgggttttttcttcttaattatttacagGCCATTGATGATGATTGCAATCAAACTGGGCAGATGATAGCAGGACTCCTCAACTGGCCTCAAGGGACTTTTGCTTCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC