Sequence
atgc intronic sequence ATGC exonic sequence...cattcttattttactgagtctggttttatgatctactttatgtggcccttgcttcttactgattcagaatattaaacaattgattgttatgcatttatagATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTATTCAG
Basic information
species | Glycine max |
transcript | GLYMA10G42960.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 13
cattcttattttactgagtctggttttatgatctactttatgtggcccttgcttcttactg---attcagaatattaaacaattgattgttatgcatttatagATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTATTCAG
| ||| | | | |||| |||| | | ||| | || |||| || || | | | ||| | || || | || | | ||||||| || || || |||| |||||||||||||| |||||||| ||||| |||||| | || ||||| || || |||| ||||||||| ||| |||||
--actatgggttatagtcatttttcttattctctatactgtaccgccat-gcgtcttgctatatatgctgtacattttataagatatcttcattgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG
upper sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G312026_T01 (Zea mays), 3'ss of exon 13
-cattcttattttactgagtctggttttatgatctactttatgtggcccttgcttcttactg---attcagaat-attaaacaattgattgttatgcatttatagATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTATTCAG
|| | | | | | | | | |||| ||||| | | ||| | || ||| || || | | | |||| | || |||| || | | ||||||| || ||||| |||| |||||||||||||| |||||||| ||||| |||||| | || ||||| || || |||| |||||||| ||| |||||
gcaactatgtgctggtcatttt--tcttattatctatactgtaccgccat-gcgtctcgctatatatgctgtacgattataagatagatt--cattgaaatgcagATTGTTGCCTTTCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATACAGCAAATTCATTGTTCAG
upper sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 13
cattcttattttactgagtct--ggttttatgatctactttatgtggcccttgcttcttactgat-tcagaatatta-aacaattgattgttatgcatttatagATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTATTCAG
|||| | || | || ||| | | | || | | || | | || | || |||| |||| |||| | | | | | | |||||||||| ||||| |||| ||| | || ||||| |||||| |||||||||||||| | |||||||| || || || ||||||||||| ||| |||||
-attcatcttgttctagttcttcaggtatctggttgctctaatattttcaagtaactgtattaatgtcaggttattgtgacaactcaattct---tacatgcagATTGTGGCTTTTCTCATCCCCCTTTTAGACGATAAATTTCCTTTGATACGAAGTATTACTTGCTGGACCCTTTCTCGGTTTAGCAAATTCATTGTTCAG
upper sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 13
--cattcttattttactgagtctggttttatgatctactttatgtggcccttgct-tcttactgattcagaatattaaacaattgattgttatgcatttatagATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTATTCAG
| | ||||| | || ||| | |||| | | || | ||| |||||||||| | || || |||| | | || | |||||||| ||||| || | || || | ||||||||||||||||| |||||||||||||| || |||||||| ||||| || |||| |||| || |||||
attacttgaattttctgtcttagagtcatataaat--ctttgtttcctatctgatgccttgctgattcagattgttgaattgttgaattgcttttatg-acagATTGTGACATTTATTATTCCCCTCTTGGATGATAAGTTTCCTCTCATACGAAGTATTTCCTGTTGGACACTTTCACGTTTCAGCAGATTTGTTGTTCAGMapped 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|192327364|gb|FK019581.1|FK019581EST: GTGCTATAGGTGAAGGTTGCATCAATGGTCTTTATCCGCATCTGTTGGAG ATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGA
genomic: GTGCTATAGGTGAAGGTTGCATCAATGGTCTTTATCCGCATCTGTTGGAGgtattttctg ... gcatttatagATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccttgcttcttactgattcagaatattaaacaattgattgttatgcatttatagATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTATTCAG
aatattaaacaattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattcttattttactgagtctggttttatgatctactttatgtggcccttgcttcttactgattcagaatattaaacaattgattgttatgcatttatagATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - -gagtctg