Sequence
atgc intronic sequence ATGC exonic sequencegtatgactcaacttgtcactgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53170.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 9
-----------------gtatgactcaacttgtcactgcttatcagctattttaaaagagtttggt----tgatt---aggctaccatgaatgaactt-ttatat-ttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
| | || ||| ||| |||| || | | | |||||| ||||| || || | ||| ||| | || || | | | |||||||| || || ||| |||||||||| ||||| |||||||| || || || |||||||| |||||||| || |||||||| |||||||||||||| ||||| |
gttctgatttctgagccctttctctaaacatgt-gttgctctgagcttaatctcacccagtttgcccttatgatttctagatcgtagtgtgttgccttgttaaacattcatagtttccctct-ttacagGCGCCATGCATTGTTTTCATTGATGAAATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCG
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 9
----gtatgactcaacttgtcactgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
||| || || | | | | || || | | | || | || | | | | |||| | | | | | || | | ||||||||||| || ||| |||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||| ||||||||||||||||||||||| |||||||
agttatatattggaaactgatatcgtccaaagaatcttatatacttgaagagaggagaatgccgcttt-agccagctttaacaatcatt-----tcctct-ttacagGCACCATGCATTGTTTTCATTGATGAAATAGATGCTGTGGGATCAACTAGGAAACAGTGGGAAGGGCACACAAAGAAGACATTGCATCAACTTCTTGTTG
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 9
gtatgactcaacttgtcactgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
|| | | | || | ||| | ||||| | | ||| | | || | ||||||| | | | |||||||| || || ||| | |||||||| ||||| |||||||| || || || |||||||| ||||||||||| ||||||||||| ||||||||||| |||||||
-gataagttattctgaaatgcaatattttatgttttactgacttaataccatgaaaacta--aaggtcaaagtaatatattttaacaatctttctctttacagGCGCCATGCATTGTCTTCATTGATGAAATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGGCACACAAAGAAGACGTTGCATCAACTTCTTGTTG
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 1
---------------------gtatgactcaact---tgtca--ctgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
|||| || || | ||| | ||| || | |||| | | | || || ||| | || | ||| ||||| | | ||| | || ||| |||||||||||||| ||||| |||||||||||||||||||| ||||||||||||||||| || || |||||||||||||||||||| ||||||||||
gtctgttgatttttgcaaatggtatccctaaattgtttgttattctggttttgcactataccacatgggtcc--tttatttatttctgattatggaatatttatttccctt--ttatctttctcta--gGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 9
gtatgactcaacttgtcactg-cttatcagctatt--ttaaaagagtttggttgattaggctaccatg-aatgaact--tttatatttaatgacgatcatg----------------tgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
|| || | | |||| || | | ||| || || ||| ||||| | |||| | | ||| || ||| | | |||| | | ||| | || |||| |||||||||||||||||||| ||||| ||||||||||| || || || |||||||||||||| |||||||||||||||||||| |||||||||||||
gtttgttgcctttggtcaatggcctctcaactgtttgttattctggtttgctaaattacttttgtacataatttccttatttgtttctaattagggacattctttttgccccatcctttttgtagGCTCCTTGTATTATTTTCATTGATGAAATAGATGCTGTTGGTTCAACTAGGAAACAATGGGAAGGTCATACAAAGAAGACATTGCACCAACTACTTGTTG
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 9
---------------------gtatgactcaacttgtcactgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
|||| | || | | | | || || | | | | | || ||| | || | ||| ||||| | | ||| | | |||| |||||||| ||||| ||||| |||||||||||||||||||| ||||||||||||||||| || || |||||||||||||||||||| ||||||||||
gtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctgttgtgacatgggtccttt-atttttttctgattatggaatatttatttccctt--ttatctttc--tgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
gtatgactcaacttgtcactgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
| | | || | ||| | | | |||| | | | | | | | | ||| | || ||| | || || | | | | |||| ||||| || ||||||||||| ||||| |||||||||||||| ||| |||| ||||||||||| |||||||| || |||||||| ||||| |||||||
-ctttatgtagatttttact-tatgtacatggtgttaattcggatatggaattggagatccattaaattttagctcattttttgt-actttcttatttcatagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
atttaat putative branch site (score: 4)
atgaatgaacttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgactcaacttgtcactgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG