Sequence
atgc intronic sequence ATGC exonic sequence...cttagccttgtgtgtagaatatacagtaaaccaaaagttcttctacgccttatgtgctcacttttcttatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
Basic information
species | Glycine max |
transcript | GLYMA13G08160.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------cttagccttgtgtg---tagaatatacagtaaaccaaaagtt--cttctacgcctta-tgtgctcacttttcttatct--------------ttctctat------------cacactttc-----tttccttgc------agAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
||| | | | || || | || | | | | || ||||| | || || ||| | | | | || | | ||||| | ||| ||| ||| ||| ||||||| || || ||||| ||||| |||||||||||||||||||| | |||||||||||||| || ||||| || || || || || ||||| || ||||
gtatctgagtacgcttcataaagtacttggtgcaagaagagtatcttggtccattttgggttactacatgaactttattagtgttttccttctgcaccatactgtctttattgctgttgtttgacagtaatgtgatttctcagtacagaaaacaaatacatattcaaatgcttctatgctgtttcagAATGTCAAGACATTTAAAGATGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAAGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCC
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------------cttagccttgtgtgtagaata----tacagtaaaccaaaagttcttctacgccttatgtgctcacttttcttatctttctctatcaca-ctttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
|| ||| | | | | || | ||| | | || || | | || | | || | | | | | || |||||||| || || ||||| ||||| |||||||||||||||||||| | ||||||||||| || || ||||| || || || || || ||||| || ||||
gtatctgattacgcttcataaaatacttgatacaagagtatcttggtccactttgggttactacaaaaacattattagtgtttttctttcgcacaatactgtcttctggttgtctgttagtaatgtgatttctcg-gtacagaaaacaaatacatattcaaatgataattctatggttttacagAATGTCAAGACATTTAAAGATGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAGGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCC
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
-cttagcc-ttgtgtgtagaatatacagtaaaccaaaagttcttctacgccttatgtgctcacttttcttatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
| | || ||| | | || || | | | | | || | | | || ||||| || ||| || ||||||||| ||||| |||||||| || || ||||||||||||||||| ||||| || || || || || || || || ||||||||||| |||||||| ||||
attcaatagttctgttcgtgttgcccttgaagccgatatatttataagagctgctccaattgtgtcatttcctaacaattatcaagtttacttgcc--gcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------------------------------------cttagccttgtgtgtagaatatacagtaaaccaaaagttcttctacgccttatgtgctcac--ttttcttatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
|||| |||| | | ||| | | | || | | | | | | | |||| ||||||| | || | || |||||||||| || || ||||||||||||||||| |||||||||||||| || || ||||||||||| ||||||||||| ||||| || | |||||||| | |
gtagatatctgatgttacgtgttttgtattatatgttttaagagtgtttctggagatttcaagtctattgagcaagttgtgcaagtgatttagagttgtattcatttcatatggaccatcctgttttttgaagcatgccagttaattgtagtcctgttatttttctctga-gtagttgcctttgctgcagAATGTTAAGACATTTAAGGATGTGAAAGGCTGTGATGATGCAAAACAGGAGCTTGAGGAAGTAGTGGAGTACCTCAAAAACCCTGCAAAGTTTACTAGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgccttatgtgctcacttttcttatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
tgctcac putative branch site (score: 2)
ctcacttttcttatct CT-rich tract
ttttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttagccttgtgtgtagaatatacagtaaaccaaaagttcttctacgccttatgtgctcacttttcttatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - tgtgtgt
- - - - - - - - - - - - - - -accaaaa
- - - - - - - - - - - - - - - - - - - - - ctacgcc