Sequence
atgc intronic sequence ATGC exonic sequencegtataacatactttcctctgtgtaatcttttatgttcaacaatttttgatgttttgtttatgcagtttcatttggccaatctttttttaatttcacagCTAAAGTTTCCATCAGCACTAGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGGAAGAGAATAGCATTGTTTCTGGATTATGATGGGACTCTTTCAC
Basic information
species | Glycine max |
transcript | GLYMA04G13880.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G13880.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G51460.2 (Arabidopsis thaliana), 3'ss of exon 1
--gtataacatactttcctctgtgtaatctttta-tgttcaacaat-ttttgatgttttgtttatgcagtttcatttggccaatctttttttaatttcacagCTAAAGTTTCCATCAGCACTAGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGGAAGAGAATAGCATTGTTTCTGGATTATGATGGGACTCTTTCAC
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gtcagtcccttactgtcctttttttcatctgaaaatatgtgccgttgttttgatgttgatagtcttctttttgttttgttttataatcctgt--tttagcagCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTTCGC
upper sequence: GLYMA04G13880.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 2
--gtataacatactttcctctgtgtaatctttta-tgttcaacaat-ttttgatgttttgtttatgcagtttcatttggccaatctttttttaatttcacagCTAAAGTTTCCATCAGCACTAGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGGAAGAGAATAGCATTGTTTCTGGATTATGATGGGACTCTTTCAC
| | |||| |||| | | | |||| | | | | | |||||||||| | | | ||| |||| || | | | ||| ||||| |||| ||||||||| || | |||||||| |||| | | | ||||||||| || ||||||||||||||||| |||||||| ||||| ||||
gtcagtcccttactgtcctttttttcatctgaaaatatgtgccgttgttttgatgttgatagtcttctttttgttttgttttataatcctgt--tttagCAGCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTT---
upper sequence: GLYMA04G13880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 1
----gtataacatactttcctctgtgtaatcttttatgttcaac--------aatttttgatgttttgtttatgcagtttcatttggccaatctttttttaatttcacagCTAAAGTTTCCATCAGCACTAGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGGAAGAGAATAGCATTGTTTCTGGATTATGATGGGACTCTTTCAC
| | | |||| ||||||| || | | ||| | || | |||| | | | |||| | || || | || || | |||| ||||| |||| |||||||||||| ||||||||| ||||| || |||| ||| || || || |||||||||||||||||||| |||||||||||||| ||||
gtaaattttgccccctttgtgttgtgtaactttggaggctcatctttgatggaaccctagatggctgactgacttagttcc---tgccctcttttcttgtgattttgcagCTTAAGTATCCATCAGCACTTAAATCTTTTGAGCAAATCACGAACTATGCCAAGGGAAAAAGAATAGCATTGTTTCTGGACTATGATGGGACTCTCTCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgatgttttgtttatgcagtttcatttggccaatctttttttaatttcacagCTAAAGTTTCCATCAGCACTAGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGGAAGAGAATAGCATTGTTTCTGGATTATGATGGGACTCTTTCAC
ttttaat putative branch site (score: 3)
tctttttttaatttc CT-rich tract
aatctttttttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataacatactttcctctgtgtaatcttttatgttcaacaatttttgatgttttgtttatgcagtttcatttggccaatctttttttaatttcacagCTAAAGTTTCCATCAGCACTAGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGGAAGAGAATAGCATTGTTTCTGGATTATGATGGGACTCTTTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA