Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaaaattcaagttcccttatctatgtccaagtatggaagttttctcgattccatttgttgatcaatgagaaactgcagATTGTGAGTGGAAGGCGCAGGCGGGCAACATCTGTGTTGCCTCGTTCGATTGGAGCTGCAGTGGGATTTGTAGATCAGCGGATAGGATGAAGGATGTTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26940.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g38050.1 (Oryza sativa), 3'ss of exon 10
---------gtaaaaaaaattcaagttcccttatctatgtccaa--gtatggaagtt--ttctcgattcca--tttgttgatcaatgagaa--actgcagATTGTGAGTGGAAGGCGCAGGCGGGCAACATCTGTGTTGCCTCGTTCGATTGGAGCTGCAGTGGGATTTGTAGATCAGCGGATAGGATGAAGGATGTTCA
| ||| | || ||| || || | || | ||| || | | | || || ||| | | | | | ||||||||||| || |||||||||||||| |||||| | || | || |||||||| ||||||||||| || || || | ||| |||||| |||||||||| || ||
tgatgaaatttcaaatcatttttttttcttttgtcaacttctgatcatattttagccaactgttggttacaaatttttcaaatggttcgcactactgcagATTGCGAATGGAAGGCGCAGGCAGGCAACGTGTGCGCCGCGTCGTTCGACTGGAGCTGCAGCGGCATCTGCAAATCGGCGGATCGGATGAAGGAGGTCCA
upper sequence: AT4G26940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G080231_T02 (Zea mays), 3'ss of exon 10
-----------------gtaaaaaaaat-tcaagttcccttatctatgtccaagtatggaagttttctcgattccatttgttgatcaatgagaaactgcagATTGTGAGTGGAAGGCGCAGGCGGGCAACATCTGTGTTGCCTCGTTCGATTGGAGCTGCAGTGGGATTTGTAGATCAGCGGATAGGATGAAGGATGTTCA
| | | | ||| | | | || | | | | ||| | || | ||| | ||||||||| |||||||||||||||||||| ||| || || ||||| ||||| ||||||||||| || || || | ||| || || |||| ||||| || ||
gttggagcgcaggagcagcagcagcgctgtcagctgaaacggttctttgcctaacacgcacaccaactc-accaagcttcgcgctcaccaaacttgtgcagATTGCGAGTGGAAGGCGCAGGCGGGGAACGCGTGCGTCGCCTCCTTCGACTGGAGCTGCAGCGGCATCTGCAAATCCGCTGACCGGATCAAGGAGGTCCA
upper sequence: AT4G26940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 10
---------gtaaaaaaaattcaagttcccttatc------tatgtccaagtatggaagttttctcgattccatttgttgatcaatgagaa--actgcagATTGTGAGTGGAAGGCGCAGGCGGGCAACATCTGTGTTGCCTCGTTCGATTGGAGCTGCAGTGGGATTTGTAGATCAGCGGATAGGATGAAGGATGTTCA
| |||||| | | | | || ||| | | || || | | | || | | | || ||||||||||||||||| || ||||| ||||||||||||||||| || || || ||||||||||| |||||||| ||||| | || ||||| | ||| || ||
aattaagtagggaaaaaaggtgatgctttggtaggagggagtatcatctgccaatgacattgttcaactaaaaattttgggatgccaatttttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACTGGAGCTGCAGCGGGATTTGCAGATCTTCTGAGAGGATCAGGGAGGTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtccaagtatggaagttttctcgattccatttgttgatcaatgagaaactgcagATTGTGAGTGGAAGGCGCAGGCGGGCAACATCTGTGTTGCCTCGTTCGATTGGAGCTGCAGTGGGATTTGTAGATCAGCGGATAGGATGAAGGATGTTCA
tgttgat putative branch site (score: 4)
aagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaaaattcaagttcccttatctatgtccaagtatggaagttttctcgattccatttgttgatcaatgagaaactgcagATTGTGAGTGGAAGGCGCAGGCGGGCAACATCTGTGTTGCCTCGTTCGATTGGAGCTGCAGTGGGATTTGTAGATCAGCGGATAGGATGAAGGATGTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG