Sequence
atgc intronic sequence ATGC exonic sequence...tgtgttaaatttcttttaaaggtatactcaataaaattatttgtcttacattcacatttttttaccgatgttattccctctgtcttgcaacaatgtttagGAAGTCCTGTTCTTGGCTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
Basic information
species | Glycine max |
transcript | GLYMA18G46420.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 4
----tgtgttaaatttcttttaaaggtatactcaataaaattatttgtcttacattcacatttttttaccgatgttattccctctgtcttgcaac--aatgtt-tagGAAGTCCTGTTCTTGGCTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
|| || ||| || | | | || | | || ||| || || || || | ||||| || | ||| |||| | || | |||| |||||||||||||| || ||||||||||| || | || || || ||||| || || ||||| ||||| || ||||| ||||||||| | ||||||||
acaaagtacaaacattcactttga--ttttctaatttgaaatatctga---acgtttg--ttcactgtccgatatttctttttctaatatgcaccttgatatcatagGTAGTCCTGTTCTTGGATATCTGGCTGCTGGTGTCCTAATCGGTCCCTATGGGCTTTCCATCATCCGTCATGTCCATGGAACAAAAGCAATTGCTGAATT
upper sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 3
-tgtgttaaatttcttttaaaggtatac-tcaataaaattatttgtcttacattcacatttttttaccgatgttattccc-tctgtcttgcaacaatgt-ttagGAAGTCCTGTTCTTGGCTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
|||| | || | | || | | ||| || || || || ||| | ||||| | || || | | | | || | || | ||||| |||||||||||||| || | ||||||||| || | ||||| || ||||| ||||| ||||| ||| | || ||||||||||| ||| | || |||||
atgtgcatacaaaagttgagaaacatctgtgattaagatcatcagtttt-catggaagtttttgt---gaccttctgcaaataaattttaccttgatatcttagGCAGTCCTGTTCTTGGATATCTTGCTGCTGGTGTCCTCATTGGTCCATATGGGCTCTCCATCATCCGTAATGTGCATGGGACAAAGGCAATTGCGGAATT
upper sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------tgtgttaaatttct----tttaaaggtatactcaataaaattatttgtcttacattcacatttttttaccg-------------atgttattccctctgtct----tgcaacaatgtttagGAAGTCCTGTTCTTGGCTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
| || | || | || | | ||| ||| ||| |||| ||| || | | || | ||| ||| | || | ||| |||| | |||| || ||||||||||| || ||||| || || ||||||||||| |||||||||||||| || |||||| | || ||||| || || || | || |||||
gtaacgtaatatattaattcactcattgtattttaaatccccatattttgtcctccttgtttcatttggacttgtactattcattgttatcatcagacaaaccatttcacttctgttgccgcaatcataatgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctatagGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
upper sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 2
-tgtgttaaatttcttttaaaggtatactcaat-aaaattatttgtcttacattcacatttttttaccgatgttattccctctgtcttgcaacaatgtttagGAAGTCCTGTTCTTGGCTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
| | | | | | || | | ||| || ||| | | | | ||| | ||| | | | || ||| || || |||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||||||| ||||| | || |||||
gcatatatatgtcactgtgccttcatttcctttcaaagtttattgccaagtttctgtactgtttcattgatagtgtgtcttccatct-gctgca-tgtttagGCAGTCCTGTTCTTGGTTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATTATTCGTCATGTACATGGGACCAAAGCGATTGCAGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacattcacatttttttaccgatgttattccctctgtcttgcaacaatgtttagGAAGTCCTGTTCTTGGCTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
gtcttac putative branch site (score: 3)
ttcacattttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgttaaatttcttttaaaggtatactcaataaaattatttgtcttacattcacatttttttaccgatgttattccctctgtcttgcaacaatgtttagGAAGTCCTGTTCTTGGCTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - cattcac