Sequence
atgc intronic sequence ATGC exonic sequence...attatcagtgcatctctcctaaattcttatttacagagcactatgctgcgaagggatttctgcattgtcttgatttatgacaagagttttttttttgcagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
Basic information
species | Glycine max |
transcript | GLYMA12G04220.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 5
-attatca-gtgcatctctcctaaattcttatttacagagcactatgctgcgaagggatttctgcattgtcttgatttatgacaagagttttttttttg--cagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
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gtttgtgatacacagaatctttgtgatgtagattttatttttttcagttttgaagttaagcatcaaaacttctgaagagctgaacttatttgtgtattggacagGTAGAAACAATTGATGACTATGATGAATACTGCCATTATGCTGCAGGACTTGTTGGTTTAGGTTTGTCAAAAATCTTCATTGCTTCGGAATTAGAAATAC
upper sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 5
-attatcagtgcatctctcctaaattcttatttacagagcactatgctgcgaagggatttctgcattgtcttgatttatgacaagagttttttttt---tgcagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
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aattgt-attgaaagta-ccaaaacttatttataagttttgtaaagaaatgaaatcatttgtttaccgatccagttgat--ccagttttcactattatacacagGTAGAAACTGTTGATGACTACGATGAATACTGCCACTATGTTGCTGGGCTTGTTGGTTTAGGTTTGTCGAAACTCTTCCTCGCTGCAGGATCAGAGGTTT
upper sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 5
attatcagtgcatctctcctaaattcttatttacagagcactatgctgcgaagggatttctgcattgtcttgatttatgacaagagttttttttttgcagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
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aatagcactagaactaaattcatctttggattatgcccaaaagttctgaaaaataaaatgtaattcacatgtgatgccgataattctactcctattgcagGTGGAAACCATTGATGACTATGATGAATATTGCCACTATGTAGCAGGACTTGTTGGATTAGGATTGTCCAAGCTTTTCCATGCCTCCAAGTTGGAAGATTMapped 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|151410377|gb|EV280192.1|EV280192EST: ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG GTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTT
genomic: ACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAGgtttgtcgca ... ttttttgcagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcgaagggatttctgcattgtcttgatttatgacaagagttttttttttgcagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
tcttgat putative branch site (score: 4)
ttttttttttgc putative PPT
aagagtttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attatcagtgcatctctcctaaattcttatttacagagcactatgctgcgaagggatttctgcattgtcttgatttatgacaagagttttttttttgcagGTAGAAACAATTGATGACTATGATGAATATTGTCACTATGTGGCGGGACTTGTTGGGCTGGGTTTATCAAAGCTTTTCCATGCGTCTGGTTCAGAAGATC
- - tcagtgc
- - - - - - -ctctcct
- - - - - - - - - - - - - - - - - - - - - atgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacaag