Sequence
atgc intronic sequence ATGC exonic sequence...tttctacattttcatgttatttatatgcatcatcaatgttttacgtcctgaaattttgtataatgcctgcttattgatgttatttctctttgcaaggaagACTCTGGTTTTGTGCCCCTATTTGTATATGCCATATTTGGGTCTTCTCGCCAGCTTGCAGTAGGTCCAGTGGCATTGGTTTCTCTCTTGGTCTCTAATGT
Basic information
species | Glycine max |
transcript | GLYMA18G52270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 2
-----tttctacattttcatgttatttatatgcatcatcaatgttttacgtcctgaaattttgtataatgcctgcttattgatgttatttctctttgcaaggaagACTCTGGTTTTGTGCCCCTATTTGTATATGCCATATTTGGGTCTTCTCGCCAGCTTGCAGTAGGTCCAGTGGCATTGGTTTCTCTCTTGGTCTCTAATGT
| | | ||| | | | | ||| | || || ||||| | | |||| |||||| | ||| | | ||||| | | | |||| | || ||||| || ||||| ||||||| |||||||| || || || || || |||||||||||||||||| | |||||||| | || || |||||
gtaagtgtttccatctctaattcctctattt---tcttctatgttctcaagtgagctcatttg-gtaatgcaaccatatcttt-tcatttccatgttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGACAACTAGCAGTAGGTCCAGTGGCACTTGTTTCTCTTCTTGTATCCAATGT
upper sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G13550.1 (Arabidopsis thaliana), 3'ss of exon 2
-------tttctacattttcatgttatttatat-gcatcatcaatgttttacgtcct--gaaattttgtataatgcctgctta---ttgatgttatttctctttgcaaggaagACTCTGGTTTTGTGCCCCTATTTGTATATGCCATATTTGGGTCTTCTCGCCAGCTTGCAGTAGGTCCAGTGGCATTGGTTTCTCTCTTGGTCTCTAATGT
|| | ||||| | | ||| | | | || | | || ||||| || ||| |||| | || |||| ||||||| | | ||||||| |||||||| ||||||| |||||||||||||| || || || ||||||||| | || || || |||||||||||||| | ||||||||||
gtgagttttattgtgaattcataggaatgctattgaagtactcctgctcttggtttaaagaaatgcctaatcatgttagctttgattcaattttataactctttg--atgcagACTCTTCATTTGTGCCGGTATTTGTCTATGCCATATTTGGCTCATCCCGTCAGCTTGCAATTGGACCTGTAGCATTGGTTTCTCTTCTCGTCTCTAATGC
upper sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g00010.t01 (Vitis vinifera), 3'ss of exon 2
tttctacattttcatgttatttatatgcatcatcaatgttttacgtcctgaaattttgtataatgcctgcttattga---tgttatttctctttgcaagga-agACTCTGGTTTTGTGCCCCTATTTGTATATGCCATATTTGGGTCTTCTCGCCAGCTTGCAGTAGGTCCAGTGGCATTGGTTTCTCTCTTGGTCTCTAATGT
| || | || | ||| ||| | | | || || | | ||||| | | | | | | | || | |||||| || || | || |||||| |||||||||| ||||||| ||||| ||||||||||| ||||||||||||||| | ||||| || ||||||||||| || |||||||||||||
-tacttgagttactagttttttctt--ctttatttatacctctttttctgaa-tcatttctgcctcttttacactggaattcttatttgtccttcttaagacagACTCCAGTTTTGTGCCTATATTTGTGTATGCAATATTTGGGTCATCTCGCCAGCTTGCAATCGGTCCTGTAGCATTGGTTTCACTACTGGTCTCTAATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgaaattttgtataatgcctgcttattgatgttatttctctttgcaaggaagACTCTGGTTTTGTGCCCCTATTTGTATATGCCATATTTGGGTCTTCTCGCCAGCTTGCAGTAGGTCCAGTGGCATTGGTTTCTCTCTTGGTCTCTAATGT
tattgat putative branch site (score: 3)
tgttatttctcttt CT-rich tract
aaattttgtataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctacattttcatgttatttatatgcatcatcaatgttttacgtcctgaaattttgtataatgcctgcttattgatgttatttctctttgcaaggaagACTCTGGTTTTGTGCCCCTATTTGTATATGCCATATTTGGGTCTTCTCGCCAGCTTGCAGTAGGTCCAGTGGCATTGGTTTCTCTCTTGGTCTCTAATGT
- -ctacatt
- - - - - -tcatgtt
- - - - - - - - - - - -tatgcat
- - - - - - - - - - - - - - - - -caatgtt
- - - - - - - - - - - - - - - - - - - - - - -tcctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcct