Sequence
atgc intronic sequence ATGC exonic sequencegtacttttattgacatttttgattaagtcatgactcttggtatctattgaaatcttctgaaatgaattcatgtgctcttgtagCATTTGCTGTTTCAAGAGACCATAAACCTGACCAAAGTGATGAGCGTGAACGGATTGAGAATGCTGGTGGTTTTGTGATGTGGGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G24940.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 4
-gtacttttattga-catttttgattaagtcatgactcttggtatcta------ttgaaatct----tctgaaatgaattcatgtgctct-----tgtagCATTTGCTGTTTCAAGAGACCATAAACCTGACCAAAGTGATGAGCGTGAACGGATTGAGAATGCTGGTGGTTTTGTGATGTGGGCAG
| | | || || | | | | || || || | |||| |||||| || | || ||| ||| | | || ||| | ||||| ||||||||||| || ||||| || || ||| | | |||| ||| ||||||||||||||||||||||||| |
gttgtgtcaaccgagcaactctatattacctattacaatttgcttctaaaatgattgaaacctcagttttgtgatgcattatttcatcttgatgatgcagCTATAGCTGTGTCAAGAGACCACAAGCCTGATCAGTCAGACGAGAGGCAGAGGATAGAGGATGCTGGTGGTTTTGTGATGTGGGCTG
upper sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 4
---------------------gtacttttattgacatttttgattaagtcatgactcttggtatctattgaaatcttctgaaatgaattc-atgtgctcttgtagCATTTGCTGTTTCAAGAGACCATAAACCTGACCAAAGTGATGAGCGTGAACGGATTGAGAATGCTGGTGGTTTTGTGATGTGGGCAG
| || ||| |||| | || | | || || | || | ||| |||| | | ||| ||| |||||||||||| || || || ||||| |||| ||||||||| | || ||||| ||||||| |||||||||||||||||||
ctactgctaagctaggagttgattctacggctgatatttcaacattggtgacaccgtttaaccactttcctaactt-----gatgcattctgcttctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgactcttggtatctattgaaatcttctgaaatgaattcatgtgctcttgtagCATTTGCTGTTTCAAGAGACCATAAACCTGACCAAAGTGATGAGCGTGAACGGATTGAGAATGCTGGTGGTTTTGTGATGTGGGCAG
tgctctt CT-rich tract
tattgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttttattgacatttttgattaagtcatgactcttggtatctattgaaatcttctgaaatgaattcatgtgctcttgtagCATTTGCTGTTTCAAGAGACCATAAACCTGACCAAAGTGATGAGCGTGAACGGATTGAGAATGCTGGTGGTTTTGTGATGTGGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG