Sequence
atgc intronic sequence ATGC exonic sequence...ggtttttagagtctttcccatgtctctgttgcaatctgtactcaactgtagaatttttcatgcaaataaaaacatgtttaattttacttgtactggacagGTAAGGTTGGAGGGTTCATTGCTTCAATTCCTGAAGTCATGGTTGCTGGTCTCCTATGCTTTATGTGGGCTATGCTTGCAGCATTGGGCTTGTCCAATCT
Basic information
species | Glycine max |
transcript | GLYMA12G30670.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30670.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G095611_T03 (Zea mays), 3'ss of exon 8
ggtttttagagtctttcccatgtctctgttgc--aatctgtactca-actgtagaatttttcatgcaaataaaaacatgtttaattttacttgta----ctggacagGTAAGGTTGGAGGGTTCATTGCTTCAATTCCTGAAGTCATGGTTGCTGGTCTCCTATGCTTTATGTGGGCTATGCTTGCAGCATTGGGCTTGTCCAATCT
|| | | | ||| ||| | | | || | |||| |||| | | |||| | | | | | || | | ||| || || || | ||||||||||| |||||||| || |||||||||| |||||| ||||| |||||||||||||| || | ||||||||||||||
-gtaagaaaactattttgcattttcatttcagtgaaaaaattctcatgctgtgagaaaaggtaatcaaaggttcttgcttatcactgttattatgactcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT
upper sequence: GLYMA12G30670.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G27810.3 (Arabidopsis thaliana), 3'ss of exon 8
---ggtttttaga-gtctttcccatgtctctgttgcaatctgtactcaactg-tagaatttttcatgcaaataaaaacatgtttaattttacttgtactggacagGTAAGGTTGGAGGGTTCATTGCTTCAATTCCTGAAGTCATGGTTGCTGGTCTCCTATGCTTTATGTGGGCTATGCTTGCAGCATTGGGCTTGTCCAATCT
|| || | || | ||| | || | |||| | || |||||| | | | || | |||| ||| || ||||||||||||||||||| | || |||||||| |||||||||||||| ||| || ||||| |||||||| ||| || | || || || | ||||| |
acaagtaactatacatcaatagcatctgaaaattagctcaactgtacaacaggtaccattttttactctctttg--actaaaacagtttttgatgtcct---cagGTAAGGTTGGAGGGTTTCTCGCATCAATTCCGCAAGTCATGGTTGCTTCTCTTCTGTGCTTCATGTGGGCAATGTTTACGGCTTTAGGTCTTTCCAACTT
upper sequence: GLYMA12G30670.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0061g01310.t01 (Vitis vinifera), 3'ss of exon 8
ggtttttagagtctttcccatgtctctgttgcaatctgtactcaactgtagaatttt----tcatgcaaataaaaacatg-tttaattttacttgtactggacagGTAAGGTTGGAGGGTTCATTGCTTCAATTCCTGAAGTCATGGTTGCTGGTCTCCTATGCTTTATGTGGGCTATGCTTGCAGCATTGGGCTTGTCCAATCT
||| | | ||| ||| | | | ||| |||| ||| ||| | ||| | || | | | | |||| | | | | |||||||| ||||||||||| ||||||||||||||||||||||||||||||| |||||| ||||| |||||||| ||||||||||||||||| ||||| ||| |
-cctttcattgactt---cataaaggtatggaggtctctacttctctgctatcctttaatttattgcccttcaaggcctaatctcatttcaatcatgttc-acagGTAAAGTTGGAGGGTTTATTGCTTCAATTCCTGAAGTCATGGTTGCTGCTCTCCTGTGCTTCATGTGGGCAATGCTTGCAGCATTGGGGTTGTCAAATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtagaatttttcatgcaaataaaaacatgtttaattttacttgtactggacagGTAAGGTTGGAGGGTTCATTGCTTCAATTCCTGAAGTCATGGTTGCTGGTCTCCTATGCTTTATGTGGGCTATGCTTGCAGCATTGGGCTTGTCCAATCT
gtttaat putative branch site (score: 4)
aatttttcatgcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtttttagagtctttcccatgtctctgttgcaatctgtactcaactgtagaatttttcatgcaaataaaaacatgtttaattttacttgtactggacagGTAAGGTTGGAGGGTTCATTGCTTCAATTCCTGAAGTCATGGTTGCTGGTCTCCTATGCTTTATGTGGGCTATGCTTGCAGCATTGGGCTTGTCCAATCT
- - - - - - ctttccc
- - - - - - - - - - -gtctctg
- - - - - - - - - - - - - - -tgcaatc
- - - - - - - - - - - - - - - - - - - - - caactgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgttt