Sequence
atgc intronic sequence ATGC exonic sequencegtaagagcatcgtttgattcattaagcaatgctaatttactttgtgagggtaacttaactgactaaaacttcttggaatgtaatgataaatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTTTTGGAAGTTGATGGCGAGAAAGCAGTTGTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G76030.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 2
gtaagagcatcgtttgattcattaagca--atgctaattt--------actttgtgagggtaacttaactgac----taaaacttcttggaatgta-atgataaatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTTTTGGAAGTTGATGGCGAGAAAGCAGTTGTGCAG
|||| | | | || | | | ||||||| | | |||| | | | | || | || | | ||| | ||| || || |||| ||||||||||| || ||||| || || || | |||||||| | | | |||||||| || |||||||||||||||| ||||| |||||||||
gtaaaggtgtgcacagttttctccaatatgatgctaactaccctgcagattttgaacagctcattctgctagcctcttatacttcctttgcttgtgtatccatcattagggcccaaagtaccaaGAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAG
upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 3
gtaagagcatcgtttgattcattaagcaatgctaattt--------actttgtgagggtaacttaactgac----taaaacttcttggaatgta-atgataaatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTTTTGGAAGTTGATGGCGAGAAAGCAGTTGTGCAG
| ||| |||| | || || | ||||||| | | |||| | | | | || | || | | ||| | ||| || || |||| ||||||||||| || ||||| || || || | |||||||| | | | |||||||| || |||||||||||||||| ||||| |||||||||
--gtgtgcacagttttctccaatatg--atgctaactaccctgcagattttgaacagctcattctgctagcctcttatacttcctttgcttgtgtatccatcattagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAG
upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 3
--------gtaagagcatcgtttgattcattaagcaatgctaatttactttgtgagggtaac----ttaactgactaaaact-tcttggaatgtaatgataaatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTTTTGGAAGTTGATGGCGAGAAAGCAGTTGTGCAG
| || ||| | | ||| | || || | | ||| || || ||| | | | | || | |||||||||||| || ||||||||||| ||||||||| | |||||||| ||||| |||||||||| || || ||||||||||| |||||||| |||||||||
gtagatttgcttttttgtcatttcttctttcttctaatacaaagtttttattggagtatagtgacacctacacactgagatgatactataactcttaaactgttcagGGTCCAAAATATCAGGAGATTGTCAATATTCGCCTTGGAGATGGCACAACGCGACGTGGTCAAGTCTTAGAAGTTGATGGGGAGAAAGCTGTTGTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgtgagggtaacttaactgactaaaacttcttggaatgtaatgataaatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTTTTGGAAGTTGATGGCGAGAAAGCAGTTGTGCAG
gactaaa putative branch site (score: 2)
aatgtaatgataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagcatcgtttgattcattaagcaatgctaatttactttgtgagggtaacttaactgactaaaacttcttggaatgtaatgataaatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTTTTGGAAGTTGATGGCGAGAAAGCAGTTGTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG