Sequence
atgc intronic sequence ATGC exonic sequence...aggcttttgaatgaagaaaaggactgttcagtgtacatgatggttgctttgatgttggactacaactcattgttgatatttatgtgttgtgcttcatcagGATAAGAATCTTTCTGGTGGCGTTTTCTTCCTTGAGCTTTTGAGTGCTGTGGAGCCAAGGGTTGTCAACTGGAGTCTTGTTACTAAAGGGGAGACTG
Basic information
species | Glycine max |
transcript | GLYMA14G00820.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G00820.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G010937_T01 (Zea mays), 3'ss of exon 12
aggcttttgaatgaagaaaaggactgttcagtgtacatgatggttgctttgatgttggactacaactcattgttgat-atttatgtgttgtgcttcatcagGATAAGAATCTTTCTGGTGGCGTTTTCTTCCTTGAGCTTTTGAGTGCTGTGGAGCCAAGGGTTGTCAACTGGAGTCTTGTTACTAAAGGGGAGACTG
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-----------------------gtgcccaacgaacaaaacttcaattcctatttttgtcagaaaactccggttgcttagtttcctgtttttccctttcagGACAAGAGCTTATCAAATGGATTGTTCTTCCTCGAGCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTG
upper sequence: GLYMA14G00820.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G382341_T01 (Zea mays), 3'ss of exon 12
aggcttttgaatgaagaaaaggactgttcagtgtacatgatggttgctttgatgttggactacaactcattgttgatatttatgtgttgtgcttcatcagGATAAGAATCTTTCTGGTGGCGTTTTCTTCCTTGAGCTTTTGAGTGCTGTGGAGCCAAGGGTTGTCAACTGGAGTCTTGTTACTAAAGGGGAGACTG
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----------gtgccgaaatgaac------atagctttaatccctattttt-tgtcagaaaact-ccggttact--tagtttcctatttttccccttcagGACAAGAGCTTATCGAATGGAATGTTCTTCCTTGATCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTG
upper sequence: GLYMA14G00820.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G04750.1 (Arabidopsis thaliana), 3'ss of exon 11
aggcttttgaatgaagaaaaggactgttcagtgtacatgatggttgctttgatgttggactacaactcattgttgatatttatgtgttgtgcttcatcagGATAAGAATCTTTCTGGTGGCGTTTTCTTCCTTGAGCTTTTGAGTGCTGTGGAGCCAAGGGTTGTCAACTGGAGTCTTGTTACTAAAGGGGAGACTG
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----------gtaaagaaaagagtcaaaccatgtaaactaaccctaatccatcttc--attaaacctaacagtt----ttgatg-gtta--ctctattagGACAAGAATCTGGCAAATGGAATCTTCTTTTTAGAGCTTTTGAGTGCTGTAGAGCCAAGAGTTGTAAACTGGAGTCTTGTATCCAAAGGAGAAACACMapped 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|163926266|gb|EH039161.1|EH039161EST: ACAATAAAGTGAAAAGAGCAGGAAGAACTTCTCAAATGGATAGTTTCAAG GATAAGAATCTTTCTGGTGGCGTTTTCTTCCTTGAGCTTTTGAGTGCTGTG
genomic: ACAATAAAGTGAAAAGAGCAGGAAGAACTTCTCAAATGGATAGTTTCAAGgtataaaacc ... gcttcatcagGATAAGAATCTTTCTGGTGGCGTTTTCTTCCTTGAGCTTTTGAGTGCTGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttgatgttggactacaactcattgttgatatttatgtgttgtgcttcatcagGATAAGAATCTTTCTGGTGGCGTTTTCTTCCTTGAGCTTTTGAGTGCTGTGGAGCCAAGGGTTGTCAACTGGAGTCTTGTTACTAAAGGGGAGACTG
tgttgat putative branch site (score: 4)
cttcatc putative PPT
attgttgatatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggcttttgaatgaagaaaaggactgttcagtgtacatgatggttgctttgatgttggactacaactcattgttgatatttatgtgttgtgcttcatcagGATAAGAATCTTTCTGGTGGCGTTTTCTTCCTTGAGCTTTTGAGTGCTGTGGAGCCAAGGGTTGTCAACTGGAGTCTTGTTACTAAAGGGGAGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- gcttttg
- - - - - - -aagaaaa
- - - - - - - - - - - - - ttcagtg
- - - - - - - - - - - - - - - - - -catgatg
- - - - - - - - - - - - - - - - - - - - - - - - - gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttg