Sequence
atgc intronic sequence ATGC exonic sequence...atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
Basic information
species | Glycine max |
transcript | GLYMA12G06980.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
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---------------gttcgtgtgaat-atagatatattc-tcatatcaccttcatataatcagaatcgttagttactgatctaa--tatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
atgcctagtaattcagattgtatttatgacctactca---ttagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG-----------------------------------
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--gtttgttaaacttcgt--taatcaaaactcgcaaaatgctagctgatatatttttatgacttatga----tcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaa-----acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
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-----ttgacgtctagattttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG
upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacct----ttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
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-tatata-tatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttca--gattggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAGMapped 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|208312127|gb|GE107347.1|GE107347EST: ATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG ACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTG
genomic: ATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAGgtgggggttc ... acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTG
EST:
gi|193540711|gb|FK494361.1|FK494361EST: AAATACAACCCTGTAAAG ACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAG
genomic: AAATACAACCCTGTAAAGgtgggggttc ... acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
atctaac putative branch site (score: 2)
cctttac putative PPT
aaattatctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG