Sequence
atgc intronic sequence ATGC exonic sequence...tattagctatcctttcccctcagatcttatagttttaccgagaaattttgcattgttgcccatcaactaaatttgccaatttttgtgtactgataaatagGAGGTGCATTAAAGCCAACTGATGTGGAGACACTGTGGGTTCACGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAAGAAAAAATGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53430.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 12
----tattagctatcctttccc---ctcagatc-ttatagttttaccgagaaattttgcattgttgcccatcaactaaatttgccaatttttgtgtactgataaatagGAGGTGCATTAAAGCCAACTGATGTGGAGACACTGTGGGTTCACGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAAGAAAAAATGGA
| | | | || | | ||| | | | ||||| ||| | |||| || || | | | | | || ||| || || |||| ||||| || |||||||| |||| || | |||||||||||||||||||||| ||||||||| | | || |||||| ||||| || |||||
tcaattctggatttcaatatctgggtgcagtttgctctctttttattgagtattttttaatcattaatcctggc---acctggtgaactttgaactattg-----tagGTGGTGCTTTGAAGCCAACAAATGTTGATAACTTGTGGGTTCACGTGACATGTGCATGGTTTCAGTCACAGGTTGCTTTTGCTAGTGATGAGCTCATGGA
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 4
------tattagctatcctttcccctcagatcttatagttttaccgagaaattttgcattgttgcccatcaactaaatttgccaatttttgtgtactgataaatagGAGGTGCATTAAAGCCAACTGATGTGGAGACACTGTGGGTTCACGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAAGAAAAAATGGA
|| ||| | | | | | | | || || | || ||| | ||| || | | | | | | || || || ||| | | ||| ||||| |||||||||| ||||| || ||| | |||||||| || || ||||||||||||| |||||||||| |||||| ||||| ||||| |||||
tcatgatactagggagcagcttcggtaaatttttttatatatatattttcattgt-tattaatgtctgtaatgttactctgaaaa-----atgatttgacacacagGTGGTGCTCTAAAGCCAACCGATGTTGACACATTATGGGTTCATGTTACTTGTGCTTGGTTTCGACCTGAAGTATCTTTTGCTAGTGATGAAAAGATGGA
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 13
--tattagctatcctttcccctcagatct-tatagttttaccgagaaattttgcattgttgcccatcaactaaatttgccaatttttgtgtactgataaatagGAGGTGCATTAAAGCCAACTGATGTGGAGACACTGTGGGTTCACGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAAGAAAAAATGGA
| | | | | | || || | || | | | || | ||| || | | | || | | | || | | | | || ||| ||||| ||||||| |||||||| || ||| |||||||||| || || ||||||||||||| |||||||| | |||||| ||||| || || |||||
ataaatgctcaagttattatcaaggagctctgcagatatgtttctac-cttggttttgatgactacaatctttttctcctaaactatttttg--gactcccagGTGGTGCTCTAAAGCCGACTGATGTTGACACATTGTGGGTTCATGTCACTTGTGCTTGGTTTCGACCTGAAGTCTCTTTTGCTAGTGATGAGAAGATGGA
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 13
tattagctatcctttcccctcagatcttatagttttaccgagaaattt-tgcattgttgcccatcaactaaat-ttgccaattt---ttgtgtactgataaatagGAGGTGCATTAAAGCCAACTGATGTGGAGACACTGTGGGTTCACGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAAGAAAAAATGGA
| | | ||| | | | || || | | | || | ||| | | ||| | || | ||| ||| || | | | || ||| ||||| |||||||| || ||||| || ||| |||||||||| || || ||||||||||||| |||||||| | |||||| ||||| || || |||||
---aaacaaagttttactatta--tcaaggagctctgctgacatgtttctaccttggttttgatgactagaatattgttcgcttaaactatttttggactcccagGTGGTGCTTTAAAGCCGACAGATGTTGACACATTGTGGGTTCATGTCACTTGTGCTTGGTTTCGACCTGAAGTCTCTTTTGCTAGTGATGAGAAGATGGA
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 13
tattagctatcctttcccctcagatcttatagttttaccgagaaattttgcattgttgcccatcaactaaatttgccaatttttgtgtactgataaat-----------agGAGGTGCATTAAAGCCAACTGATGTGGAGACACTGTGGGTTCACGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAAGAAAAAATGGA
| |||| || || ||| || | ||| || || | | || | ||| |||||| | | | ||||| ||| ||||| |||||||||||||| | |||||| | |||||||| || || |||||||||||||| |||||||| | ||| ||||||| ||||| |||||
-------cagaatttctttcaggagtttcc--tttggtttggagacttta-gttactgacaacgaagaacattctttgattttt-tttgtggttaaatttctttctcttagGTGGTGCTCTAAAGCCAACTGATATTGAGACATTATGGGTTCATGTCACTTGTGCTTGGTTTCAACCTGAAGTTTCTTTCTCAAGTGATGAAAAGATGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgcattgttgcccatcaactaaatttgccaatttttgtgtactgataaatagGAGGTGCATTAAAGCCAACTGATGTGGAGACACTGTGGGTTCACGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAAGAAAAAATGGA
tactgat putative branch site (score: 2)
aactaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattagctatcctttcccctcagatcttatagttttaccgagaaattttgcattgttgcccatcaactaaatttgccaatttttgtgtactgataaatagGAGGTGCATTAAAGCCAACTGATGTGGAGACACTGTGGGTTCACGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAAGAAAAAATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - cctttcc
- - - - - - - - - - - - - - - - - - - cgagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaaa