Sequence
atgc intronic sequence ATGC exonic sequence...ttgacatgtctattgtttgtttttaccttgaaccaattgcttatctacattctgtattttcactttgctaaccgggggtgttattttttttatgaaacagGGAATCCTGAAGGTTTGGGCACTGAGCTATTGGAAACCCTAGTGAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTTAAAAACTATGACGGCGATCT
Basic information
| species | Glycine max |
| transcript | GLYMA01G40080.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40080.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g10680.1 (Oryza sativa), 3'ss of exon 2
--ttgacatgtctattgtttgtttttaccttgaaccaattgcttatctacattctgtattttcactttgctaaccgggggtgttattttttttatgaaacagGGAATCCTGAAGGTTTGGGCACTGAGCTATTGGAAACCCTAGTGAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTTAAAAACTATGACGGCGATCT
|| ||| | ||| | | | | | | |||| | | || | || | | |||| || || ||| |||| ||| ||||| | |||| | ||| || |||||||| |||| |||||||||||||||||||||||||| | ||||| | |||| || || |
ttttttcattgcggcatactgtaaat-ctgtaatttagtatgccatctctacatgagggtgtccagtgaatatgtgtaatttctattgttcttttgag-cagGCAATGCTGAATGCCTGGGGAGTGAACTTTTGGAAACATTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTGAAACTACGAGACTACAGTGGTGACTT
upper sequence: GLYMA01G40080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G872264_T01 (Zea mays), 3'ss of exon 3
ttgacatgtctattgtttgtttttaccttgaaccaattgcttatctacattctgta-ttttcactttgctaaccgggggtgttattttttttatgaaacagGGAATCCTGAAGGTTTGGGCACTGAGCTATTGGAAACCCTAGTGAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTTAAAAACTATGACGGCGATCT
| | | || |||||| || || || || | |||| | | || | | ||| | | | | | |||| ||||||| || ||||| |||||| ||||| || ||||| || |||| |||||||||||||||||||||||||| | ||||| || | ||| | | ||
tctgttgctgttttagctgttttgacgtttaaaatataaatc-tctataaaatatagctcataaaccattaatttgtcatttctactgtattattaaacagGCAACACTGAATATTTGGGGACTGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAAACTACAAGATTATAATGATGACAC
upper sequence: GLYMA01G40080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G075921_T01 (Zea mays), 3'ss of exon 2
-----ttgacatgtctattgtttgtttttaccttgaaccaattgcttatctacattctgtattttcactttgctaaccgggggtgttattttttttatgaaacagGGAATCCTGAAGGTTTGGGCACTGAGCTATTGGAAACCCTAGTGAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTTAAAAACTATGACGGCGATCT
| | ||| | |||| | || | || | | | || | | | | ||| | | | | | |||| ||||||| || ||||| ||||||| || || || ||||| || |||| |||||||||||||||||||||||||| | | ||| | | ||| | || ||
ccattgcattaggcctactatttgatgtt----taaaatataaatctttataaaata-gagctcatggggcattaatttgtcatttctactgtattatcaaacagGCAACGCTGAATGTTTGGGGACAGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAGACTACGAGATTATAATGGTGACGC
upper sequence: GLYMA01G40080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G090693_T01 (Zea mays), 3'ss of exon 2
-ttgacatgtctattgtttgtttttaccttga--accaattgcttatctacattctgtattt--tcactttgctaaccgggggtgttattttttttatgaaacagGGAATCCTGAAGGTTTGGGCACTGAGCTATTGGAAACCCTAGTGAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTTAAAAACTATGACGGCGATCT
|| || | | || | | || | || | || | ||| ||| | | |||| || | | | | || ||| ||| ||||||| ||| ||||| | |||| | || | ||||||||| | || |||||||||||||| ||||||||||| | || ||| ||||| | ||| ||
acatactgctccaggatgtgcagtcagctacatgacagcattctaaactattgtctagttctactcacaatgtttattgctgctgacattcttt-----aaacagGCAATGCTGAATGCCTGGGTGCGGATTTGTTGGAAACCTTGGTAAAGATGGCTCCTACGAAAGAGGAAGAACTGAAGCTTCGAAACTTTACCGGGGACTC
upper sequence: GLYMA01G40080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0129g00220.t01 (Vitis vinifera), 3'ss of exon 2
ttgacatgtctattgtttgtttttaccttga-accaattgcttatctacattctgtattttcactt-tgctaaccgggggtgttattttttt-tatgaaacagGGAATCCTGAAGGTTTGGGCACTGAGCTATTGGAAACCCTAGTGAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTTAAAAACTATGACGGCGATCT
|| | | || | | | | || | ||| | | | || || | || || | | ||| || ||||| | || |||| || || ||| | ||||| ||||||| |||||||| |||| ||||||||||| || || |||||||| ||||||||| | | || || || |
---gaattaaaacagattatatgtccattaatgttcatttaatgcttgctttgcaaataattgtttgtggggatcctaagtgaaatatttttgtctgtggcagGTAACCCAGAAAGCTTGGGTGCTGAGCTTTTGGAAACTTTAGTAAAGATGGCTCCCACCAAGGAGGAAGAAATAAAACTTCGAGATTACAGTGGTGACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacattctgtattttcactttgctaaccgggggtgttattttttttatgaaacagGGAATCCTGAAGGTTTGGGCACTGAGCTATTGGAAACCCTAGTGAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTTAAAAACTATGACGGCGATCT
tgctaac putative branch site (score: 1)
ttatttttttt putative PPT
tgttattttttttatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgacatgtctattgtttgtttttaccttgaaccaattgcttatctacattctgtattttcactttgctaaccgggggtgttattttttttatgaaacagGGAATCCTGAAGGTTTGGGCACTGAGCTATTGGAAACCCTAGTGAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTTAAAAACTATGACGGCGATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- -acatgtc
- - - - - - -tgtttgt
- - - - - - - - - - - - -ccttgaa
- - - - - - - - - - - - - - - - -caattgc
- - - - - - - - - - - - - - - - - - - - - - - -cattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggggtg
