Sequence
atgc intronic sequence ATGC exonic sequence...gattgaaaattgagttatcccccttccaattgatacaataggtatcttttatactttaaatgtttaaagtttaattatttgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
Basic information
species | Glycine max |
transcript | GLYMA09G08830.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 6
---gattgaaaattgagttatccccctt-ccaattgatacaataggtatcttttatactttaaatgtttaaagtttaattatttgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
|||| | | | | || || || || || | | || | || | | | | | | | ||||||| ||||||||| |||||||||||||| |||||||| || |||||||| || |||||||| | | ||| || ||||| | || || | ||| | || |||
ccaaattgtcctgagcatcctttctgttatcagttctagatatgaaaatgcctcgtttttgacatatctgatccgtgg--aactattggctgtatgttg--cagCAAAGTCATGGATGTCTTCATTAAGGCTGCAGAGTATATGGAGATGCCAGTCCGGCGCAGTGACGATGAACCCTTGCAGAAATTATTTGTAGCTGTTAGG
upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G167868_T01 (Zea mays), 3'ss of exon 5
-gattgaaaattgagttatcccccttccaattgatacaataggtatctt--ttatactttaaatgtttaaagtttaattatttgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
| ||| | ||| | |||| | ||| || | || || | | | | || || | |||| |||||||||| ||||||||||||||||||||||| ||||||||||| || ||||| || | | |||||| ||||| |||||||| | ||| | || ||
ttccgggaaacttctatattgggtctt-aatttacttgctagccttcaaaatcatgtttcattttcccttgcctgatccatgggttgtttccatgtc--acagCAAAGTTATGGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTTCAAAAATTGTTTGTAGCTGTTAGA
upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
--gattgaaaattgagttatcccccttccaattgatacaataggtatcttttatactttaaatgtttaaagttta-attatttgtgaata--ttatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
| || | | | || || || | | | || |||| | | |||||| || | | ||| | || | |||||||||| || |||||||||||||||||||| ||||||||||| || ||||| || | | |||||| ||||| || ||||| | ||| | || ||
tagcttccagg--aaacttctatttttggtgttaatttacttgctagctttcgaaatc---atgtttttcccttgtgtgagccatgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA
upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79940.3 (Arabidopsis thaliana), 3'ss of exon 6
gattgaaaattgagttatccccct-----tccaattgatacaataggtatcttttatactttaaatgtttaaagtttaattatttg--------tgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
| | ||| | | || ||| | | ||| |||| | || ||| | | | ||||| |||| || | || | || || | |||| ||||||||| ||||| || |||| |||||| ||||| || ||||| |||||||| |||||||||||||| |||||||| || ||||| ||||||| || |||
----gtatattcactcatacccatatacattcaagtgatgctattggtgcatgacaaatgggctgtgttttc-gtttgtttgtatgacatgttttaaaatttttattgtccagCAAAGTTATGGAAGTTTTCACCAAGGCAGCTGAGTACATGGAGATTCCAGTTCGTAGAACTGATGATGAACCTCTGCAGAAGCTCTTTATGTCTGTTAGG
upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
gattgaaaattgagttatcccccttccaattgatacaataggtatcttt-tatactttaaatgtttaaagtttaattatt----tgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
||||| || || | || | || | || | | | | | ||| || | ||| ||| |||| ||||| | | ||| ||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||||||||| ||||| | || || ||||| || || || ||||| ||||||
----gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctat-tataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttatactttaaatgtttaaagtttaattatttgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
gtttaat putative branch site (score: 4)
atactttaaatgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattgaaaattgagttatcccccttccaattgatacaataggtatcttttatactttaaatgtttaaagtttaattatttgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
- - - - - - - - atccccc