Sequence
atgc intronic sequence ATGC exonic sequencegtgggtttttctcccataatatctgtgttatagattgtgttgtaaaacgtagaaatgctcatcatatgcctttccatggaaatatgcagGTGAACAGTGGGGTGTTGAGCGTGTGCACAGCTTTCTTATCAGGAGAGCCTGCAACGAGATTGCGTTCACAGGAACTGCAGCAACTAATCGCGGCACTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16340.1 |
intron # | 29 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 29
lower sequence: GRMZM2G462803_T04 (Zea mays), 3'ss of exon 7
------gtgggtttttctcccataatatctgtg----ttatagattgtgttgtaaaacgtagaaatgctca--tcatatg------cctttccatggaaatatgcagGTGAACAGTGGGGTGTTGAGCGTGTGCACAGCTTTCTTATCAGGAGAGCCTGCAACGAGATTGCGTTCACAGGAACTGCAGCAACTAATCGCGGCACTGC
|| | | | | || | |||| | | | | | || || | || |||| | | |||||||| ||||||||||| || || |||||||| || |||||||| || ||||| ||||| || | | || || ||||||||||| || ||||| ||| |||
gtgaggctgaatctactttttgcagaattcggaagatttatgagtgtcactaccgtttgctcattttcttgcttcttttggccaattcttttgacatcaccatgcagGTCAACAGTGGGGTATTAAGTGTGTGCACTGCATTCTTATCTGGCGAGCCAGCAACTAGGCTCAGATCCCAAGAACTGCAGCAGCTCATCGCCGCATTGC
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 29
lower sequence: GLYMA15G28340.1 (Glycine max), 3'ss of exon 2
-----------gtgggtttttctcccataatatctgtgttatagattgtgttgtaaaacgtagaaatgctca-tcatatgcctttccatggaaatatgcagGTGAACAGTGGGGTGTTGAGCGTGTGCACAGCTTTCTTATCAGGAGAGCCTGCAACGAGATTGCGTTCACAGGAACTGCAGCAACTAATCGCGGCACTGC
| |||| | | || | | | | ||||| | | || | ||| | | | | | | |||||||||| ||||| || ||||| || ||||| || ||||| || || |||||||| || || || || |||||||||||||||||||| || || || || |
gttttaaaaacattggttgataattc-tatttttggcctcccagatttgaatattttacttttggtctttcaattctgtcagcacacttctctttgtgcagGTGAATAGTGGAGTCTTGAGTGTCTGCACTGCCTTCTTGTCCGGGGAGCCTGCGACCAGGTTACGATCACAGGAACTGCAGCAACTTATAGCTGCCCTTC
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 29
lower sequence: Vv11s0016g00100.t01 (Vitis vinifera), 3'ss of exon 29
---------gtgggtttttctcccataatatctgtgttatagattgtgttg-taaaacgtagaaatgctcatcatatgcctttcca-tggaaatatgcagGTGAACAGTGGGGTGTTGAGCGTGTGCACAGCTTTCTTATCAGGAGAGCCTGCAACGAGATTGCGTTCACAGGAACTGCAGCAACTAATCGCGGCACTGC
| ||| ||| | | | | | || ||| | | | ||| | |||| | || | | |||||||||||||||| ||| |||| |||||||| || || | || || ||||||||||| || ||||||| ||||| || |||||||| || || || || |
agaccatattttcatttgtcttcatctagtttagcaagactatctgaattgatccctccttcctatggcattaatatcaggacaaactgcacttttgcagGTGAACAGTGGAGTGCTGAGTGTGTGCACGGCCTTTCTTTCGGGTGAGCCTGCAACAAGGCTGCGTTCCCAGGAGCTTCAGCAACTCATTGCTGCCCTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgttgtaaaacgtagaaatgctcatcatatgcctttccatggaaatatgcagGTGAACAGTGGGGTGTTGAGCGTGTGCACAGCTTTCTTATCAGGAGAGCCTGCAACGAGATTGCGTTCACAGGAACTGCAGCAACTAATCGCGGCACTGC
ttgtaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtttttctcccataatatctgtgttatagattgtgttgtaaaacgtagaaatgctcatcatatgcctttccatggaaatatgcagGTGAACAGTGGGGTGTTGAGCGTGTGCACAGCTTTCTTATCAGGAGAGCCTGCAACGAGATTGCGTTCACAGGAACTGCAGCAACTAATCGCGGCACTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG