Sequence
atgc intronic sequence ATGC exonic sequencegtctggtcttttttcgttttgaagcatttgatatgaacagtaagagctattagctattgtatgactgttcacacttctttcaacttgtcttctcttttcatttcttaacagGACTTAAAGAATGCAAAGTCCATTGTTGACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G24810.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g48770.2 (Oryza sativa), 3'ss of exon 5
gtctggtcttttttcgttttgaagcatttgatatgaacagtaagagctattagctattgtatgactgttcacacttctttcaacttgtcttctcttttcatttcttaacagGACTTAAAGAATGCAAAGTCCATTGTTGACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAA
|||| | || | | || |||| | ||| || || | | || ||| | || ||||| || ||||||||||| || | ||||| |||||||| ||||| || || || || |||||||| || ||||||||||||||||||||||| || ||||
-------------------------gtttgcctctattctgaaaaa--acggacttatgtaaaa-tgtgcaggattgctata--------tcattttcttaatgttgtcagGATTTGAAGAATGCAAAATCATTAGTTGAATGGATTGCATGGGCAGAGCCTCAATATAATTTTAACCCGATGATAGATGAATGGTGCAAGGAGGCACCAA
upper sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 6
gtctggtcttttttcgttttgaagcatttgatatgaacagtaagagctattagctatt-gtatgactgttcacacttctttcaacttgtcttctcttttcatttcttaacagGACTTAAAGAATGCAAAGTCCATTGTTGACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAA
|| | || | | || ||||| |||| | || | | | ||| ||| | ||||| | ||||||||||| || | |||| ||||| |||||||| || || ||||| |||||||||| ||||| ||||||||||||||||| |||||||
---------------------------------------gttt-atctctaacctgcaagtatg-ctgtctagcacagttggagtccattacatttttctattggtggccagGATCTGAAGAATGCAAAATCATTGATTGAATGGATAGCGTGGGCAGAGCCTCAGTATGATTTTAATCCGATGATTGATGAATGGTGCAAGGAGGCTCCAA
upper sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G20110.1 (Glycine max), 3'ss of exon 5
gtctggtcttttttcgttttgaagcatttgatatgaacagtaagagctattagctattgtatgactgttcacacttctttcaacttgtcttctcttttcatttcttaacagGACTTAAAGAATGCAAAGTCCATTGTTGACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAA
||| | | || | | |||| ||| | | | || | | || | | ||||||| ||||| | || || ||||||||||| ||||| ||||| ||||||||||||||||| ||||| || ||||| || || |||||||| ||||| |||||||||||||| |||||||| |
---------gtttgcttcttttatcctttgggatgtatggatatagaggt---ccatggaac--------------ctttcaaaaggtctttgtacctacatttttttcagGACTTAAAAAATGCGAAGTCAATTGTTGACTGGATTGCATGGGCTGAGCCACAATATAACTTTAATCCTATGATCGATGAATGGTGCAAAGAAGCTCCTA
upper sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G24420.1 (Glycine max), 3'ss of exon 4
gtctggtcttttttcgttttgaagcatttgatatgaacagtaagagctattagctattgtatgactgttcacacttctttcaacttgtcttctcttttcatttcttaacagGACTTAAAGAATGCAAAGTCCATTGTTGACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAA
|||| | | | ||| | || | | || || | || | | ||| |||| ||||||||||| ||||| ||||| ||||| ||||||||||| ||||| || || || || || |||||||| ||||| |||||||||||||| |||||||| |
-------------------------gtttgcttcttttatcctttgggatttatggatatagaggtccatggagcctttcaaaaggtttttgtacctacatatcttt-cagGACTTAAAAAATGCGAAGTCAATTGTCGACTGGATTGCATGGGCTGAGCCGCAATATAACTTTAATCCTATGATCGATGAATGGTGCAAAGAAGCTCCTA
upper sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g02740.t01 (Vitis vinifera), 3'ss of exon 4
gtctggtcttttttcg--ttttgaagcatttgatatgaacagtaagagctattagctattgtatgactgttcacacttctttcaac-------ttgtcttctcttttcatttctta------acagGACTTAAAGAATGCAAAGTCCATTGTTGACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAA
|| | | | ||| | |||| | ||| || ||||| | || || | ||| |||| |||| | || |||| || | | | || || || ||||||||||||||||||||||| || | ||||||||| || ||||| |||||||| || | || || || ||||| ||||||||||||| ||||| || |
gttttgcatgcttttggattttaagatgattgtgataggaagtaatatctgtt-gtcattatatggttgttgggcatcctatcaaaaaaaaaattatatggttgttgggcttactattggttgcagGACTTAAAGAATGCAAAGTCAATAGCTGACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtatgactgttcacacttctttcaacttgtcttctcttttcatttcttaacagGACTTAAAGAATGCAAAGTCCATTGTTGACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAA
cacttctttcaacttg CT-rich tract
ttttcatttcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctggtcttttttcgttttgaagcatttgatatgaacagtaagagctattagctattgtatgactgttcacacttctttcaacttgtcttctcttttcatttcttaacagGACTTAAAGAATGCAAAGTCCATTGTTGACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA