Sequence
atgc intronic sequence ATGC exonic sequence...gcataattaacattacatgtagttttatcaagctggattagttgtacaattcacacatttctcttctcttaatctgttattctttttgattgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
Basic information
species | Glycine max |
transcript | GLYMA01G44330.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G44330.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G115456_T01 (Zea mays), 3'ss of exon 1
----gcataattaacattacatgtagttttatcaagctggattagttgtacaattcacacatttctcttctcttaatctgttattctttttgattgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
|| || || | | | | | ||| || || || || ||| || | | | | | | | | | | || | | ||||| |||||||||||||| ||||| ||||||||||||||||||| || ||| | ||||| | || || || | || | ||||| || ||||| |
tcacatatgatctgcactctac-tggcaattggaagatg--ctattttctcagcaaacaatttatattgcaccctaac-gatgtcatctgtgcctttttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: GLYMA01G44330.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
gcataattaacattacatgtagtt--ttatcaagctggattagttgtacaattcacacatttctcttctcttaatctgttattctttttgattgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
| ||||| || || || | ||| | ||||| || || | ||| | | | | ||| | | | | || | | ||||| |||||||||||||| ||||| ||||||||||||||||||| || ||| | ||||| ||||||| || | || | ||||| || ||||| |
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaac--gatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: GLYMA01G44330.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
-gcata-attaacattacatgtag---ttttatcaagctggattagttgtacaattcacacatttctcttctctta-atctgttattctttttgattgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
| || | || || |||| | | ||| ||| | ||| | ||| | || || || || || ||| || || |||||||||||||| ||||| ||||| || ||||| |||||||| || || ||||||||||| |||| ||| | |||| ||||| |||| ||| |||
tgtttatacaaatcttctatgttggcttcctattgcaacggaatccaagta-acttcttgcggttgatgactgttccattctccatgcttcttttttt-----cagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
upper sequence: GLYMA01G44330.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
gcataattaacattacatgtagtttta---tcaagctggattagttgtacaattcacacatttctcttctcttaatc-tgttattctttttga---ttgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
|| | || | | | || |||||| || || || ||| |||| || || | || || || | || ||| |||||||| ||||| ||||| || || ||||||||||||||||||||||||||| | ||||| ||||||||| | || ||||| ||| | ||| ||
----tgttggcttttcttcttcccctaaattcaagcaacatcgttt---cagttcttcaatttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
upper sequence: GLYMA01G44330.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
gcataattaacattacatgtagttttatcaagctggattagttgtacaattcac--acatttctcttctcttaatctgttattctttttgattga--caagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
| ||| | | | | | || | ||| |||| | | | | || |||| ||| || | || || | ||| ||||| ||||| ||||| || ||||| || ||||||||||||||||| || ||| |||||||| ||||||| ||||| || ||||| |||||||| |||||
----atgcgctattttgttaattgtcttgaatattatttatttgtgtttgtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaattcacacatttctcttctcttaatctgttattctttttgattgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
gattgac putative branch site (score: 3)
ttattctttttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcataattaacattacatgtagttttatcaagctggattagttgtacaattcacacatttctcttctcttaatctgttattctttttgattgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - acatgta
- - - - - - - - - - - - - - caagctg
- - - - - - - - - - - - - - - - - - - - - - - - - tcacaca