Sequence
atgc intronic sequence ATGC exonic sequence...ctctgcgaaaaaacgacgaaacaaaaatgtgataaaactgagttcctacagaaaaaaagcacagacttgagtataaaatgtctgtcttaatgctctgcagGTTTTACTAGTACCATCAGCTTTCACCAAGGTCACTGGGGAGGCACACTGGGAGATTCTTCTTCGAGCCCGAGCAATTGAAACTCAATGTTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G08790.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G08790.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g31830.1 (Oryza sativa), 3'ss of exon 5
---------------------------------ctctgcgaaaaaacga--cgaaacaaaaatgtgataaaactgagttcc-tacagaaaaaaagcaca---gacttgagtataaaatgtctgtcttaatg--ctctgcagGTTTTACTAGTACCATCAGCTTTCACCAAGGTCACTGGGGAGGCACACTGGGAGATTCTTCTTCGAGCCCGAGCAATTGAAACTCAATGTTAT
| || | | || || | ||| ||| ||||| ||| || ||| | | ||||| | | | || || | |||| |||||||||||||| || ||||| || || ||||||||||| |||||||| |||||||| ||||| || || ||||| || ||||| |||
gtagtgatttatggcattatactgacataagtttttcctgattgccttatcctaagcatacctgtcatatctctgaggaaagctcaggtgaattgcatattgttttccagtattcttctaatatgccagtgacctttttagGTCTTACTAGTACCATCCGCGTTCACAAAAGTAACTGGGGAGGCGCACTGGGAAATTCTTCTCCGAGCTCGTGCCATTGAGACACAATGCTAT
upper sequence: AT4G08790.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G145578_T01 (Zea mays), 3'ss of exon 5
--------ctctgcgaaaaaacg--acgaaacaaaaatg--tgataaaactgagttcctacaga---aaaaaagcacagacttga-gtataaaatgt----ctgtcttaat---gctctgcagGTTTTACTAGTACCATCAGCTTTCACCAAGGTCACTGGGGAGGCACACTGGGAGATTCTTCTTCGAGCCCGAGCAATTGAAACTCAATGTTAT
| | || | || || | || ||| | || | | || | || | | | |||| ||| || ||||| ||| |||||||||| | |||| |||||||| ||||| || ||||| ||| | || || |||||||||||||| ||||| || ||||| || |||||||| || |||||||||
gtggttacacattctaatatacttcacacagtcaatatgattcattatattggatgccctcctatcatagaaagtgtagagcagatgtatattttgtgatcctgtcttaattttgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGGGAAATTCTCCTCCGAGCTCGTGCAATTGAGACACAATGTTAT
upper sequence: AT4G08790.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G43950.1 (Glycine max), 3'ss of exon 5
ctctgcgaaaaaacgacgaaacaaaaatgtgataaaactgagttcctacagaaaaaaagcaca-gacttgagtataaaatgtctgt--cttaatgctctgcagGTTTTACTAGTACCATCAGCTTTCACCAAGGTCACTGGGGAGGCACACTGGGAGATTCTTCTTCGAGCCCGAGCAATTGAAACTCAATGTTAT
|| || ||| || | | ||||| | ||| | || | | |||| | ||| || | | ||||| |||| || || |||| ||||| | || || || || ||||||||||||||||||||||| ||||| |||||||| |||||||| |||
--------------------gtaataa-gtggaaatattactttcctgcttaaatcggttgtttgtctacaatctaaattttcttatgttttacaacatccagGTACTACTGGTGCCTGCAGCATTCACAACAGTAACAGGTGAAGCACACTGGGAGATTCTTCTTCGTGCCCGTGCAATTGAGACTCAATGCTAT
upper sequence: AT4G08790.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G38690.1 (Glycine max), 3'ss of exon 7
ctctgcgaaaaaacgacgaaacaaaaatgtgataaaactgagttcctacagaaaaaaagcacagacttgagtataaaatgtctgt---cttaatgctctgcagGTTTTACTAGTACCATCAGCTTTCACCAAGGTCACTGGGGAGGCACACTGGGAGATTCTTCTTCGAGCCCGAGCAATTGAAACTCAATGTTAT
|| || ||| || | | ||||| | |||| | | || | | |||| | | | || | | ||||| |||| || || |||| ||||| | || ||||| || ||||| ||||||||||||||||| ||||| | |||||| |||||||| |||
--------------------gtaataa-gtggaaatattactttcctgcttaaaatgggtt--gtctacaatctaaatttttcttgtgttttacaacatccagGTACTACTGGTGCCTGCAGCATTCACAACAGTAACTGGTGAAGCACATTGGGAGATTCTTCTTCGTGCCCGTGTAATTGAGACTCAATGCTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctacagaaaaaaagcacagacttgagtataaaatgtctgtcttaatgctctgcagGTTTTACTAGTACCATCAGCTTTCACCAAGGTCACTGGGGAGGCACACTGGGAGATTCTTCTTCGAGCCCGAGCAATTGAAACTCAATGTTAT
tcttaat putative branch site (score: 3)
agtataaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctgcgaaaaaacgacgaaacaaaaatgtgataaaactgagttcctacagaaaaaaagcacagacttgagtataaaatgtctgtcttaatgctctgcagGTTTTACTAGTACCATCAGCTTTCACCAAGGTCACTGGGGAGGCACACTGGGAGATTCTTCTTCGAGCCCGAGCAATTGAAACTCAATGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
ctctgcg
- - - -aaaaaac
- - - - - - - gacgaaa
- - - - - - - - - - -caaaaat
- - - - - - - - - - - - - - - -ataaaac
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacagac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaat