Sequence
atgc intronic sequence ATGC exonic sequence...cattcttattttactgagtctggttttgtgatctacattatgtggcccttgcttcttactaattcagaatattaaacaattcattgttttgcatttatagATTGTGGCATTTCTTATCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTGTTCAG
Basic information
species | Glycine max |
transcript | GLYMA20G24040.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G312026_T01 (Zea mays), 3'ss of exon 13
-cattcttattttactgagtctggttttgtgatctacattatgtggcccttgcttcttacta---attcagaat-attaaacaattcattgttttgcatttatagATTGTGGCATTTCTTATCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTGTTCAG
|| | | | | | | | | || | ||||| | | | ||| | || ||| ||| || | | | |||| | || ||| || || ||||||| || ||||| ||||| |||||||||||||| |||||||| ||||| |||||| | || ||||| || || |||| |||||||| |||||||||
gcaactatgtgctggtcatttt--tcttattatctatactgtaccgccat-gcgtctcgctatatatgctgtacgattataagatagattcattgaaat--gcagATTGTTGCCTTTCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATACAGCAAATTCATTGTTCAG
upper sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 13
cattcttattttactgagtctggttttgtgatctacattatgtggcccttgcttcttacta---attcagaatattaaacaattcattgttttgcatttatagATTGTGGCATTTCTTATCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTGTTCAG
| ||| | | | || | |||| | | | ||| | || |||| ||| || | | | ||| | || || | | | | ||||||| || || || ||||| |||||||||||||| |||||||| ||||| |||||| | || ||||| || || |||| ||||||||| |||||||||
--actatgggttatagtcatttttcttattctctatactgtaccgccat-gcgtcttgctatatatgctgtacattttataagatatcttcattgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG
upper sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 13
cattcttattttactgagtct--ggttttgtgatctacattatgtggcccttgcttcttactaat-tcagaatatta-aacaattcattgttttgcatttatagATTGTGGCATTTCTTATCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTGTTCAG
|||| | || | || ||| | | | || | | || | | || |||| |||| |||| |||| ||| | | || || | |||||||||| ||||| ||||| ||| | || ||||| |||||| |||||||||||||| | |||||||| || || || ||||||||||| |||||||||
-attcatcttgttctagttcttcaggtatctggttgctctaatattttcaagtaactgtattaatgtcaggttattgtgacaactcaat-tcttaca--tgcagATTGTGGCTTTTCTCATCCCCCTTTTAGACGATAAATTTCCTTTGATACGAAGTATTACTTGCTGGACCCTTTCTCGGTTTAGCAAATTCATTGTTCAG
upper sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 13
--cattcttattttactgagtctggttttgtga-tctacattatgtggcccttgcttcttactaattcagaatattaaacaattcattgttttgcatttatagATTGTGGCATTTCTTATCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTGTTCAG
| | ||||| | || | | | ||| || | | ||| ||| || ||||||| | || || || | | || || | |||||||| ||||| |||| || || | ||||||||||||||||| |||||||||||||| || |||||||| ||||| || |||| |||| ||||||||
attacttgaattttctgtcttagagtcatataaatctttgtttcctatctgatgc--cttgctgattcagattgttgaattgttgaattgcttttatg-acagATTGTGACATTTATTATTCCCCTCTTGGATGATAAGTTTCCTCTCATACGAAGTATTTCCTGTTGGACACTTTCACGTTTCAGCAGATTTGTTGTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccttgcttcttactaattcagaatattaaacaattcattgttttgcatttatagATTGTGGCATTTCTTATCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTGTTCAG
tactaat putative branch site (score: 1)
aatattaaacaattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattcttattttactgagtctggttttgtgatctacattatgtggcccttgcttcttactaattcagaatattaaacaattcattgttttgcatttatagATTGTGGCATTTCTTATCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - -gagtctg
- - - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - ctacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caattca