Sequence
atgc intronic sequence ATGC exonic sequence...tattttgattggttaatctttacactgatagtgtattaaaactcattgatttatatagcaaaaaaaatagggatatttaagggattatttgaatttgcagGACGAAAGGAGAGCGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTGGAGCAGCTCGTGGCTTGAGATACCTTCACGAAGAATGTAGAGTGGGTTG
Basic information
species | Glycine max |
transcript | GLYMA08G03340.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G03340.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 5
---tattttgattggttaatctttacactgatagtgtattaaaactcattgatttatatagcaaaaaaaatagggatatttaagggattatttga--atttgcagGACGAAAGGAGAGCGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTGGAGCAGCTCGTGGCTTGAGATACCTTCACGAAGAATGTAGAGTGGGTTG
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cagttgttcaaggtactatgtcttgcaccaacaatggagtgaaagttagtaattt-tactgtaaactaat---gtatgtt-aagatatcattgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
upper sequence: GLYMA08G03340.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G480607_T02 (Zea mays), 3'ss of exon 5
---tattttgattggttaatctttacactgatagtgtattaaaactcattgatttatatagcaaaaaaaatagggatatttaagggattatttgaatt----tgcagGACGAAAGGAGAGCGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTGGAGCAGCTCGTGGCTTGAGATACCTTCACGAAGAATGTAGAGTGGGTTG
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ttctctctctgtttcactttttttgtaccaagggtcc-tgcgagcctagtgatgt------tgacatatatctgtcctgttaagctattttttgaaatatcattcagGTCATAATCGAGAAACATTGGAGTGGACTGCACGACAAAAGATTGCAGTTGGTGCTGCTCGTGGGCTGCGGTACCTTCACGAGGAATGTAGGGTTGGCTG
upper sequence: GLYMA08G03340.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 4
-----tattttgattggttaatctttacactgatagtgtattaaaactcattg--atttatatagcaaaaaaaatagggatatttaagggattatttgaatttgcagGACGAAAGGAGAGCGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTGGAGCAGCTCGTGGCTTGAGATACCTTCACGAAGAATGTAGAGTGGGTTG
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caaactaaagtcatgtttcaatatccactctaactttgtaatgaaccatactattactgttgtggctgagaaaaccaagttttctgttgg-------gaattttcagGACGTGATCGAGGTCTGCTAGAATGGTCTGCACGACAAAAAATTGCAGTTGGAGCTGCTCGAGGATTGAGATATCTTCATGAAGAATGCAGAGTGGGTTGMapped 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|26269266|gb|CA820329.1|CA820329EST: CTAGTTTATGAGTACATCTGCAATGGCTCTCTGGATTCTCATATCTACA GACGAAAGGAGAGCGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTG
genomic: CTAGTTTATGAGTACATCTGCAATGGCTCTCTGGATTCTCATATCTACAgtaaattcct ... gaatttgcagGACGAAAGGAGAGCGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatttatatagcaaaaaaaatagggatatttaagggattatttgaatttgcagGACGAAAGGAGAGCGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTGGAGCAGCTCGTGGCTTGAGATACCTTCACGAAGAATGTAGAGTGGGTTG
cattgat putative branch site (score: 4)
aaaaaaaatagggata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattttgattggttaatctttacactgatagtgtattaaaactcattgatttatatagcaaaaaaaatagggatatttaagggattatttgaatttgcagGACGAAAGGAGAGCGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTGGAGCAGCTCGTGGCTTGAGATACCTTCACGAAGAATGTAGAGTGGGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - gatagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa