Sequence
atgc intronic sequence ATGC exonic sequence...cttcatatatttgagtgttgggaaaatcagttaaaggattgttttgtctttttgtgtgtggtgcaatgttcataactgtttgttttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
Basic information
species | Glycine max |
transcript | GLYMA03G41180.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 6
----cttcatatatttgagtgttgggaa-aatcagttaaaggattgttttgtctttttgtgtgtggtgcaatgttcataactgtttgttttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
| || ||| | | || | | | || | | || | || | | | || | ||| |||| || | | ||| ||||||| ||||| ||||||||||| | ||| | ||| |||||| | |||||||||| ||||||||| || ||||| || ||||| || |||||| ||| ||
tgaggattctacgattggacctggtcaatgactattggtagtgatttgctggatgcctgcatctcattcatc--tgctaatcgtttattatgt--aatt-ttcagCTGAGACTGTAATATACAGAATCTTTTATTCCATAAATAGAGCTGGAAATGGCCATCTTACCCTCAGAGAGCTAAAACGTGGGAATTTAATTGCTGCGAT
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 6
-cttcatatatttgagtgttgggaaaatcag-ttaaaggattgttttgtctttttgtgtgtggt-gcaatgttcataactgtttgttttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
||| ||| | | | || ||||| || || ||||||| | ||| || | || ||| || | ||| || | | |||| || ||||| ||||||||||| | ||||| ||| |||||||| || ||||| | ||| || ||||| ||||| || |||||||| |||||| |||| |
aactcaactatctattttgttttaagatcagatttgctgaatgttttgaactgttgctaatgtttgctgtgt-cacattcatttcttgatgtt--ttcttcagCGGAGACTGTAATATACAGAATCTTTTACTCCATAAATAGATCTGGGAATGGTCATCTGACTCTGAGAGAGCTCAAACGTGGAAATTTAATTGCTGCACT
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------cttcatatatttgagt--gttgggaaaatcagttaaaggattgttttgtctttttgtgtgtg-gtgcaatgttcataactgtttgtttttt---ccaatggcc-cagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
|||| ||| | | | | | || | |||| | | || | | || || | | ||| | | ||| | |||| ||||||||||||| ||||||||||||||||||||||| ||||| |||||||| | ||||||| |||| ||||||||||| ||||| || |||| |||||
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgtaatgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 5
cttcatatatttgagtgttgggaaaatcagttaaaggattgttttgtctttttgtgtgtggtgcaatgtt-cataactgtttgtttt---ttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
| | | | ||| | | | ||| || | | || ||| ||| | ||| | ||| || ||| ||||||||||||||| |||||||||| ||||||||| |||||||| || ||||| || |||| | ||||||||||| || |||||| |||||||||| ||
----gaaaaaaaaaaaatctggagcttgtttatgaatcatgtattttgatgaaacagctgatgctatgctacatgctgatacaatttgcattttgatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 6
------cttcatatatttgagtgttgggaaaatcagttaaaggattgttttgtctttttgtgtgtggtgcaatgttcataactgtttgttttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
| ||||| || || || | | | || | | ||||| | || | ||| || ||||| |||| | || ||||||||||||||| ||| |||||| ||| ||||| |||||||| || ||||| || |||| | ||||||||||| || |||||| |||||||||| ||
tctggagtccatattctttggtatttgctgctaccggtatcaaag----ctaaatttttaaggatgcttttctgtctgatacaatttgtattttgc--tgaaacagCTGAAACTGTCACCTACCGAATATTTTATTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctttttgtgtgtggtgcaatgttcataactgtttgttttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
tcataac putative branch site (score: 2)
ttttttcca putative PPT
tttgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcatatatttgagtgttgggaaaatcagttaaaggattgttttgtctttttgtgtgtggtgcaatgttcataactgtttgttttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - -tgttggg
- - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaatg