Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagaacgactctaatcatacgtcttgctgttgtagttggttcctcctctcatgattaaaacacatacacagGCGCTGTCGAAGATCACGTCTACGGGTGCTATGACTTTCTGTTTTATTCAAGCAATTGAACGCAGCGCACAAGGCACAACCTATGGAAGCCTTCTGAATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G02170.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G02170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0021g00990.t01 (Vitis vinifera), 3'ss of exon 5
----------------gtaagtagaacgactctaatcatacgtcttgctgttgtagttggttcctcctctcatgattaaaa----------cacatac--------------acagGCGCTGTCGAAGATCACGTCTACGGGTGCTATGACTTTCTGTTTTATTCAAGCAATTGAACGCAGCGCACAAGGCACAACCTATGGAAGCCTTCTGAATT---
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gtaagtttcggaatgactgattagacatagtcc--ttatatatcttattttcccaattgtttcaagacctcagaccaaaaagctaaatatgtgtatactgatttctttgggaacagGCATTATCACAAATTACATCAACTGGTGCTATGACTTTCTGTTTCATCCAAGCAATTGAGCG-GGGGCACGCAGCT--ACATATGGAAGCGTCCTAAATGCAA
upper sequence: AT1G02170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S65_2V6.3 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------------------------gtaagta-gaacgactctaatcatacgtct--tgctgttgtagtt----ggttcctcctct----catgattaaaacacata------------cacagGCGCTGTCGAAGATCACGTCTACGGGTGCTATGACTTTCTGTTTTATTCAAGCAATTGAACGCAGCGCACAAGGCACAACCTATGGAAGCCTTCTGAATT---
| ||| | | | | ||| || | | | |||| | | |||| | | | ||| | |||| | || | | | |||| ||||| ||||||||||| || ||||| ||||| ||||| ||||||||||| |||||| | || || | ||| ||||| || | ||
gtatgtaagttgcctttgtaaattacgaaccttggtgtcattctattgtaacaccacctttgtaattttacgggtcagaagttaaaattgcaagcatgtatgtgtctgatgctgtatttagtgctctcggagtttgaagatgcatccacaggtacatgtctctgacgcttgatggatttttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAAGCGATTGAAAGGGGC---CACGCTCAAACGTATGGTAGTTTATTGTGCGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacgtcttgctgttgtagttggttcctcctctcatgattaaaacacatacacagGCGCTGTCGAAGATCACGTCTACGGGTGCTATGACTTTCTGTTTTATTCAAGCAATTGAACGCAGCGCACAAGGCACAACCTATGGAAGCCTTCTGAATT
atgattaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagaacgactctaatcatacgtcttgctgttgtagttggttcctcctctcatgattaaaacacatacacagGCGCTGTCGAAGATCACGTCTACGGGTGCTATGACTTTCTGTTTTATTCAAGCAATTGAACGCAGCGCACAAGGCACAACCTATGGAAGCCTTCTGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG