Sequence
atgc intronic sequence ATGC exonic sequencegtatcaatatctttgctttaaccacttttttttatctggtttcttgactctctcatattgtgaacataagGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G24570.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------gtatcaatatctttgctttaaccacttttttttat-ctggtttcttgactctctcatattgtgaacataagGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA
|| | | | | ||| | | ||| |||| | ||||| | | | || | | ||||||||||| ||| | || |||| || |||||||| |||| ||| || |||||||||||||||||||| || || || ||||| || ||||||||||||
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------gtatcaatatctttgctttaaccacttttttttatctggtt-tcttgactctctcatattgtgaacataagGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA
|||| | | | ||| | | ||| |||| | || | ||||| | | || | | ||||||||||| ||| | || |||| || |||||||| |||| ||| || |||||||||||||||||||| || || || ||||| || |||||||| |||
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------------gtatcaatatctttgctttaaccacttttttttatctggtttcttgactctctcatattgtgaacataagGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA
|| | | || | | | | | | | | | | | | | |||| | ||||||||||| ||| | || |||| || |||||||| |||| ||| || ||||| || ||||||||||| || || || ||||| || ||||||||||||
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgcttattcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------gtatcaatatctttgctttaaccacttttttttatctggtttcttgactctctcatattgtgaacataa---------------gGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA
||| | | | || | || | || || || | | | | ||||| | | ||| |||||||||| ||| | || |||| || |||||||| |||| ||| || ||||| || ||||||||||| || || || ||||| || |||||||||||
gtaagaatccattgcgctcgatcataaatattggatgacatattttccttgcaactcttaccatcattattgtttgcctaactaaagtcaaaagtgttctgctaattcaatcatgttatgatattaagcatttaatttttttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAG
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------gtatcaatatctttg-----ctttaacca-cttttttttatctggtttcttgactctctcatattgtgaacata----agGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA
|| ||| | | | || || || | || | | | | | || || | || ||| | | ||||||||||| || ||||| |||| || |||||||| || | ||| || |||||||| || |||||||| ||||| |||||||| || ||||||||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------gtatcaatatctttg-----ctttaacca-cttttttttatctggtttcttgactctctcatattgtgaacata----agGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA
|| ||| | | | || || || | || | | | | | || || | || ||| | | ||||||||||| || || || |||| || |||||||| || | ||| || |||||||| || |||||||| ||||| |||||||| || ||||||||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttaaccacttttttttatctggtttcttgactctctcatattgtgaacataagGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA
tcttgac putative branch site (score: 3)
acttttttttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcaatatctttgctttaaccacttttttttatctggtttcttgactctctcatattgtgaacataagGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG