Sequence
atgc intronic sequence ATGC exonic sequence...acacataatcatacctatgctgactttgtactaggtttatgtgagattttcttgatagaatacatgtgttggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
Basic information
species | Glycine max |
transcript | GLYMA13G31260.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 6
acacataatcatacctatgctgactttgtactaggttta---tgtgagattttcttgatagaatacatgtgttgg--cacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
| ||| | | |||| | || || | | | ||| | | || ||| ||||||| | | | | | |||| |||| ||||||||||||||||||||||| |||||||| || ||| || || | ||||||||||||||||| || || ||||| |||||||||||||| ||||||
---tagaatttggaacttaccagcttttcattattttaagatcgcaatattgcaatatttgactac-tgtgttgagtctgactgtgtcatatcatggctatt-agGTTTTTGTGGAGGAAGAATGCTACTTTTGCTATCTCTCGGCACTACAAACGCTTTGATGTATTTGAAGAAGCAGAAGCTAATAAAGCTGCTGGCAAGTAT
upper sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G044866_T01 (Zea mays), 3'ss of exon 6
---acacataatcatacctatgctgactttgtactaggtttatgtgagattttcttgatagaatacatgtgttggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
| ||| || || || | | | | | | ||| || || || | || || | | | | ||| || | ||||||| | |||||||||||| | ||||||||||| ||| ||||| | |||||||||||| |||| || || ||||| || |||||||||||||||||
gtatcccatcattgtag-tacgacatttatttgactgatccatgaaag-ttgggctgctgtaagtgata-atgagtaatctgatttctcactctacctgttagGTTCCTTTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTTGAAGAAGCAGAAGCGAACAAAGCTGCTGGAAAGTAC
upper sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
acacataatcatacctatgctgactttgtactaggtttatgtgagattttc-ttgatagaatacatgtgttggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
| | ||||| | || | | ||| | | | || ||| | || || | || || | | | | | || || | | |||| ||||| |||||||||||||| | ||||||||||| ||| ||||| | |||||||||||| || | || || ||||| || ||||||||||||||||||
gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctgtaactgataaggagcaatctgatttcttactctgcatatt-agGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT
upper sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
acacataatcatacctatgctgac--tttgtactaggtttatgtgagattttcttgatagaatacatgtgt-tggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
| | | || | | || |||| | | | | || | | || | | | | ||| |||| || || | | || || ||||||||||| ||||| |||||||| || |||| |||||| | ||| |||||||| || || || ||||||||||||||||||||||| || |||
---agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT
upper sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
--acacataatcatacct--atgctgactttgtactaggtttatgtgagattttcttgatag-aatacatgtgttggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
||| || | || || || | | || | | | | || || ||| |||| | || || ||||| | || ||| || ||||| |||||||||| ||||| | ||||||||| |||| ||||||||||||||||||||| ||||| || || || |||||||||||||||| ||||||
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaat----cctattctt-ttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttcttgatagaatacatgtgttggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
cattaat putative branch site (score: 3)
ttctcatccttattt putative PPT
attaattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acacataatcatacctatgctgactttgtactaggtttatgtgagattttcttgatagaatacatgtgttggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA