Sequence
atgc intronic sequence ATGC exonic sequencegtgctaagttatttcacatgtgttgcagaggttacttgtttatattttagttcttgatattttcatttattattttgcttgatagAGGATGCATGAGTGTGCTGAACAAGGACTTGCTGCACATTGGCTTTACAAGGAAACTGGCAATCCTTTTTTATCCATAGACAGCATGGATGAACCTGAAA
Basic information
species | Glycine max |
transcript | GLYMA01G43940.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G43940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G106931_T01 (Zea mays), 3'ss of exon 12
gtgctaagttatttcacatgtgttgcagaggttacttgtttatattttagttcttgatattttcatttatt-attttgcttgatagAGGATGCATGAGTGTGCTGAACAAGGACTTGCTGCACATTGGCTTTACAAGGAAACTGGCAATCCTTTTTTATCCATAGACAGCATGGATGAACCTGAAA------
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-------------gtaaataattttgtgcccttatttgaataaattctgatagttcatgttgatgctgatggaggtctcttcacagCGAATGCATGAGTATGCAGAACATGGACTTGCTGCTCATTGGCTGTATAAGGAGA---GCAAAG---TTGAGTACAGAAGTAGCATGAGTAAGAGAATAAGACAAA
upper sequence: GLYMA01G43940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0039g02260.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------------------------------------gtgctaagttatttcacatgtgt-tgcagaggttacttgtttatattttagttcttgatattttcatttattattttgcttgat-agAGGATGCATGAGTGTGCTGAACAAGGACTTGCTGCACATTGGCTTTACAAGGAAACTGGCAATCCTTTTTTATCCATAGACAGCATGGATGAACCTGAAA
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gtaccacacctacagattccataatctcatgtcaagcttatttctaaatggttttgattcagctaacaataatagttgctttatcttttcagagggaaagaataatcgcgtgtcaagcttatttgtaaatgcttttgatttagctaacaataatagttgctttattttttcagAGGATGCATGAGTATGCGGAACATGGACTTGCTGCACATTGGCTTTATAAAGAGACCGAAAACAAATTGCCTTCCACGAGCATCTTAGATGACTCTGAAAMapped 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|5760041|gb|AI965404.1|AI965404EST: CAGTCCAAGGTCCTGACAACTCACCTTTAGAAGTACAAATAAGGACACAG AGGATGCATGAGTGTGCTGAACAAGGACTTGCTGCACATTGGCTTTACAAG
genomic: CAGTCCAAGGTCCTGACAACTCACCTTTAGAAGTACAAATAAGGACACAGgtgctaagtt ... tgcttgatagAGGATGCATGAGTGTGCTGAACAAGGACTTGCTGCACATTGGCTTTACAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttacttgtttatattttagttcttgatattttcatttattattttgcttgatagAGGATGCATGAGTGTGCTGAACAAGGACTTGCTGCACATTGGCTTTACAAGGAAACTGGCAATCCTTTTTTATCCATAGACAGCATGGATGAACCTGAAA
tcttgat putative branch site (score: 4)
ttttgctt putative PPT
tttatattttagttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctaagttatttcacatgtgttgcagaggttacttgtttatattttagttcttgatattttcatttattattttgcttgatagAGGATGCATGAGTGTGCTGAACAAGGACTTGCTGCACATTGGCTTTACAAGGAAACTGGCAATCCTTTTTTATCCATAGACAGCATGGATGAACCTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA