Sequence
atgc intronic sequence ATGC exonic sequencegtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G02960.4 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g38800.1 (Oryza sativa), 3'ss of exon 6
gtaagctcattgaagcttcttccttttttctttttcttttattttttgt---ctca--gttgcatttaag---ttgtaacaccaaaccacaaaattgtc--tgattcttatttt-----agCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
|| || || |||| | ||||| | | | || || ||| | |||| |||| || || || | || || ||| | | || | | | | | |||| | || || ||||||||||||||||| || ||||||||||||||||||||| |||||||| | || ||||| |||| ||||||
gttagtcttgtgttccttccccactttttttatcttattggttctttctgagctcaatgttgacttaaaaatctttttttacatgacttaaaatctattaatgttcttcaatgtccaacagCTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAG
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g36740.4 (Oryza sativa), 3'ss of exon 6
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
| | | || | | ||||| ||| || | | || | | |||||||||||| | || ||||||||||||||||||||||| || ||||| | || || | |||||| ||||||
------------------------------------------------------------------cttcattgtgcatttcactagttgctgatctttaac--agttgtttcttttgagggctgctggatttttgctgccatgctatatcatggcttgggctattagTATCATGCAACGTCAAAGACAAAGACAG
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------------gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaa-----accacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
||| | ||||| | || |||| | | | || || ||| || ||||| | || | || | | ||||| ||| || | | || | | |||||||||||| | || ||||||||||||||||||||||| || ||||| | || || | |||||| ||||||
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggc-aagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaac--agTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 7
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
|| || | | ||| || | | | || || || ||| |||| || |||| | | | | | | | | || ||| ||||| | || | || |||||||||||||| || |||| |||||| ||||||||||| | ||||| | |||||||| |||||| |||||
gtgagtgaaagaatgctctttaactatctggttatcattgttttgttgta-catcatcattagaagt-tggtattgatgctcta--ttacttgac---------agCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
| | | |||| | | | | |||| | | |||||| ||| || || | | ||||| | ||| | || |||||||| || || ||||| | ||| |||||||||||||| |||||||| | |||||||| ||||||||||||
------------------gtaagtgaaataaccatcttgaaaaatatatt---gttggcaatgtataataacacttgtttttttaatggtttgcaattgaa---agCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G118957_T05 (Zea mays), 3'ss of exon 2
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
|| | | ||| | |||| || ||| | | | || | | | | |||| | |||| | || | |||| ||||||||| | || ||||||||||| ||||||||||| || ||||| | ||||| | |||||| ||||||
-------------------------gttagcgatcgatacattgcatatctcctgtgttttttt-tggcgatgtaaagttaattgactctgctggtctt-tggcagCTATTTCTTTTGAGAGCCGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 5
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
|| | || | ||| | | |||| || ||| || | | || | | | | | | || | |||| | || | |||| ||||||||| | || ||||||||||| ||||||||||| || ||||| | ||||| | |||||| ||||||
-------------------------gttagtgattaatacattgtatatctcctgtgtttttttgtcg--atgtaaagttaactgactctgttggtatt-tgacagCTATTTCTTTTGAGAGCGGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 5
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaac-cacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
|| || | | | || | || | | ||| | || | |||| | || || || | | | || | || | || | | ||||| | ||||| || |||| ||||||||||| |||||| | || |||||||||||||||||||| ||||||||| | || ||||| |||| |||||
gtgag-tgactttagttcattagggataagtggttcatatagtagttgtattgctttcaaatacatcattgggctaacctcatcacatggcc--attctc--tgcagCTTTTCTTGCTTCGAGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 6
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaacca-caaaattgtctgattcttatttt----agCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
|| || | ||| || || | ||| || ||||| | | ||| ||| || || || || | ||| | ||| ||| | | |||||| ||||| || |||| || |||||||||||||| | || ||||| |||||||||||||| ||||||||||| ||||| || |||| |||||
gtgag-tgatttgagtttttctttttagtcaaattcttccaatgtttt-----attgatttcaaaatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 5
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaacca-caaaattgtctgattcttattt-tagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
| | ||| | ||| |||| | | || | | | | ||||||| || | | | | | | |||| | | | ||||| || |||| || |||||||| |||||| | || |||||||||||||||||||| ||||||||| | || ||||| |||| |||||
-----gtgagtgactttagttcattttggataagtggttaacacagtatttgtattgcattcaaat-acattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA
upper sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G11960.1 (Glycine max), 3'ss of exon 6
gtaagctcattgaagcttcttccttttttc---tttttcttttattttttgtctcagttgcatttaagttgtaacaccaaacc-acaaaattgtctgattcttattt-tagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
||||| |||| || | ||| || || ||| | | ||| | | ||| || || || || | | || || ||| || | | || | | ||||| || |||| || || ||||||||||| | || ||||| |||||||||||||| ||||||||||| ||||| || |||| |||||
gtaagtgatttgagttttttctttttagtcaagttcttcccatgtccaatgtttta-ttgatttcaaaatgcaatgcagagcccacctaatctgctcactattttctgcagCTTTTCTTGCTTCGTGCCGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
ttcttatttt CT-rich tract
tgattcttatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA