Sequence
atgc intronic sequence ATGC exonic sequence...tgtttatacaaatcttctatgttggcttcctattgcaacggaatccaagtaacttcttgcggttgatgactgttccattctccatgcttctttttttcagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G02990.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g63750.1 (Oryza sativa), 3'ss of exon 1
tgtttatacaaatcttctatgttggcttcctattgcaacggaatccaagtaacttcttgcggttgatgac-tgttccattctccatgcttctttttt--tcagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
| ||| || || | | | | | | | || || | | || | | | | | | | |||| || | | || | ||||| ||||| |||||||||||||| | ||||||||||||||||| || ||| | ||||| |||||||| |||| |||| || | | | |||||
--atcatataacact-cagtcagaagtacttgtaccgggcagatacactgtgccatgtacgttagccggcctctaacgatctcattggtgcacttatgagcagGGATTTAGGAAAGTTGATCCAGATAGGTGGGAGTTTGCAAACGAAGGTTTTCTTAGAGGACAAAAGCATCTACTGAAGACCATCAACAGAAGGAAACCAA
upper sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
tgtttatacaaatcttctatgttggcttcctattgcaacgga--atccaagtaacttcttgcggt-tgatgactgttccattctccatgcttctttttttcagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
|| || | || | | ||| | || | | || || | || | | | | | || | ||| || ||||| |||||||| |||||||||||| | ||||| |||||||| ||||| ||| | ||||| ||||| || | || |||| ||| | | | |||||
ccttaatttga--tttgcac-tcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G115456_T01 (Zea mays), 3'ss of exon 1
tgtttataca-aatcttc--tatgttggct-tcctattgcaacggaatccaagtaacttcttgcggttgatgactgttccattctccatgcttctttttttcagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
| | | | |||| | | | |||| | | || || || || ||| || | || || |||||| ||||| |||||||| |||||||||||| | ||||| |||||||| ||||| ||| | ||||| || ||||| | || |||| ||| | | | |||||
---tcacatatgatctgcactctactggcaattggaagatgctattttctcagcaaacaatttatattgcaccctaa-cgatgtcatctgtgcctttttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G44330.1 (Glycine max), 3'ss of exon 1
tgtttatacaaatcttctatgttggcttcctattgcaacggaatccaagta-acttcttgcggttgatgactgttccattctccatgcttcttttttt-----cagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
| || | || || |||| | | ||| ||| | ||| | ||| | || || || || || ||| || || |||||||||||||| ||||| ||||| || ||||| |||||||| || || ||||||||||| |||| ||| | |||| ||||| |||| ||| |||
-gcata-attaacattacatgtag---ttttatcaagctggattagttgtacaattcacacatttctcttctctta-atctgttattctttttgattgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
upper sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G01190.1 (Glycine max), 3'ss of exon 1
tgtttatacaaatcttctatgttggcttcctattgcaacggaatccaagta-acttcttgcggttgatgactgttccattctccatgcttctttttttca----gGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
| | || | || || || | || ||| ||| | ||| | ||| | || || || || | | ||| | || || |||||| ||||| ||||| ||||| || ||||| |||||||| || || ||||||||||| |||| ||| | |||| ||||| |||| ||| |||
-gcat-tattagcattacat-ttagttt--tatcaagctggattagttgtacagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
upper sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
------tgtttatacaaatcttctatgttggcttcctattgcaacggaatccaagtaacttcttgcggttgatgactgttccattctccatgcttctttttttcagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
| ||| | ||| ||| | | ||| | ||| ||||| | | | ||| |||| || ||| | ||||| ||||| || || ||||||||||||||||| |||||||| ||||| ||| ||||||| ||||| || | | ||||||||| |||||||| |
atgcgctattt-tgttaattgtcttgaatattatttatttgtgtttgtgatcaa--aacttagt-ttctaaggggtagtttttttcttca--ctttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagtaacttcttgcggttgatgactgttccattctccatgcttctttttttcagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
ctgttccattctccat CT-rich tract
ttcttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttatacaaatcttctatgttggcttcctattgcaacggaatccaagtaacttcttgcggttgatgactgttccattctccatgcttctttttttcagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - -atacaaa
- - - - - - - - - - - - - - - - - - - - -aatccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcttc