Sequence
atgc intronic sequence ATGC exonic sequence...tgtcttatatgctgtgtgtttctaatgatgttgcttcatcgacacctttatgtatattgttcctactgggaagtttgaacttttggttaattactaacagAAAGCAGACGGGCTTCTGTTGATATCTTCTTAAAGGCAGCTGGGTATCTTGACTGTGCTGTAAGGCATGTTCTTCCACAGTTGCCTGGCGAACTCAG
Basic information
species | Glycine max |
transcript | GLYMA20G35900.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G131969_T04 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------------tgtcttatatgctgtgtgtttctaatgatgt-tgcttcatcgac--acctttatgtatattgttcctactgggaagtttgaacttttggttaattactaacagAAAGCAGACGGGCTTCTGTTGATATCTTCTTAAAGGCAGCTGGGTATCTTGACTGTGCTGTAAGGCATGTTCTTCCACAGTTGCCTGGCGAACTCAG
| |||| || |||||||| | | | ||| ||| |||| ||| | || | | || || | | ||| ||||| || |||||||| |||||||| ||||||| ||||||||||| || || |||||||| || ||||||| || || || |||| || || ||
gtactgcaactgtttgttaactgcaaatccgaggtgcggtgtcgttgcctcggagactgcggctccaagtttcctccctttaaattatgccatgaaacacgctaatgatttgtcgtgcattgacgtacctcggccaatacttctcatgcgctgataaggcgacatatttccaatgtgctacagAGAGTCGACGGGCTACTGTTGATGTCTTCTTGAAGGCAGCTGGATACCTAGACTGTGCAGTTCGGCATGTACTCCCGAAGATGCCACTGGAGCTAAG
upper sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------tgtcttatatgctgtgtgtttctaatgatgttgcttcatcgacacctttatgtatattgttcctactgggaagtttgaacttttggttaattactaacagAAAGCAGACGGGCTTCTGTTGATATCTTCTTAAAGGCAGCTGGGTATCTTGACTGTGCTGTAAGGCATGTTCTTCCACAGTTGCCTGGCGAACTCAG
|||| | | | | | | |||||| || ||| | | | | | || || ||| | | || ||||||| | | || ||||| |||||| |||| |||||||||||||||| |||||||| |||||||| ||||| || | ||||||||| || ||||| ||| || | ||
gttaggcttctctgagaaactttctcatccatcttctcatacagtctcttgaccattttttatgcaatgattttttttc-ttaaaaaaagggta-aggtttctcagacttaacattatggttgtttggtttttcatta-tagAAAACAGACGAACTTCGATTGATATCTTCTTAAAAGCAGCTGGATATCTTGATTGTGCCGTTAAGCATGTTCTCCCCCAGTTTTCTGCTGAGCAAAG
upper sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G73390.2 (Arabidopsis thaliana), 3'ss of exon 6
tgtcttatatgctgtgtgtttctaatgatgttgcttcatcgacacctttatgtatattgttcctactgggaagtttgaac------ttttggttaattactaacagAAAGCAGACGGGCTTCTGTTGATATCTTCTTAAAGGCAGCTGGGTATCTTGACTGTGCTGTAAGGCATGTTCTTCCACAGTTGCCTGGCGAACTCAG
| || | ||||| | | | || | | || | | | || || | | ||| | ||| || | ||| | ||||| || || ||||| | |||||||||||||| |||||||| || || ||||||||||| | |||||||||||| || || | ||| | ||
-----tgtaatgtccatgttttccactgtctcaattagtata-actgtaagatgtaatggttatgtccttcagtcttaacgatatgcttgtttcaatcttttctagAAAATAGGCGAGCTTCAATCGATATCTTCTTAAAAGCAGCTGGATACCTGGACTGTGCTGTGAAGCATGTTCTTCCTCATTTTTCAACCGAGCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttatgtatattgttcctactgggaagtttgaacttttggttaattactaacagAAAGCAGACGGGCTTCTGTTGATATCTTCTTAAAGGCAGCTGGGTATCTTGACTGTGCTGTAAGGCATGTTCTTCCACAGTTGCCTGGCGAACTCAG
ggttaat putative branch site (score: 4)
ttaattactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcttatatgctgtgtgtttctaatgatgttgcttcatcgacacctttatgtatattgttcctactgggaagtttgaacttttggttaattactaacagAAAGCAGACGGGCTTCTGTTGATATCTTCTTAAAGGCAGCTGGGTATCTTGACTGTGCTGTAAGGCATGTTCTTCCACAGTTGCCTGGCGAACTCAG
- - -tatatgc
- - - - - - tgtgtgt
- - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - -cgacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttttgg