Sequence
atgc intronic sequence ATGC exonic sequencegtaatatgacctccattttctcttgaaaacaaattcaaatgttttccatcttcaatacttacttactttctatgcatttacgatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05030.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 9
-------gtaatatgacctccattttct----cttgaaaacaaattcaaatgttttcca----tcttcaatacttacttactttctatgcatttacgatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
|||| ||||| |||| || | | | | | | | | | ||| ||||||| || | || || | |||||| || ||||| ||| |||| || | |||||||||||| | ||||| || ||||| |||||||||||||| || || |||||| || | ||||||
gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacct---cagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 10
gtaatatgacctccattttctct-tgaaaacaaattcaaatgttttccatcttcaatacttacttactttctatgcatttacgatgag--acagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
|||| | | |||| | || | | | | | |||| || | | | | | | || |||| |||||||||||||||| || ||||||||| || | ||||||||| | || || || ||||| |||||||||||||| |||||||| |||| | || || |
gtaagtagcttcataccttctgtatggacatttgcttttgatcatgcattctttggtaatgcttatgctaatgttctattg-gatggatcacagGCATGCCTTTGCAACATTGTCGTTTATCTCCGAGACTTTTCTGTTTCTTTATGTTGGTATGGATGCATTGGATATAGAGAAGTGGAAGATTGTCGGTCAA
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 7
gtaatatgacctc--cattttctcttgaaaacaaattcaaatgttttccatcttc-aatacttacttactttctat----gcatttacgatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
||||| ||| |||||| || | | ||| | | | || | ||| || ||| | || || | | ||| | | | ||||||||||||||||||||||| || |||||||||||||| | ||||| || ||||| |||||||| | ||||| ||||| ||| || | ||||||
gtaattattccttgtcattttttcgctagtaatgtttctgttctgcttaataaacgaatgctgactgaattccttttgggcctttttcattcacttagGCATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGAC
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G311165_T01 (Zea mays), 3'ss of exon 9
gtaatatgacctccattttctct-tgaaaacaaattcaaatgttttccatcttcaatacttacttactttctatgcatt-tacgatgag--acagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
|||| | | |||| | || | | | | | |||| || | |||| | ||| | | | |||| |||||||||||||||| || ||||||||| || ||||||||| | || || || ||||| |||||||||||||| |||||||| |||| | || || |
gtaagtagcttcataccttctgtatggacatttgcttttgatcatgcattctttggtaat-gcttatgcta-atgtactattggatggatcacagGCATGCCTTTGCAACATTGTCGTTTATCTTCGAGACTTTTCTGTTTCTTTATGTTGGTATGGATGCATTGGATATAGAGAAGTGGAAGATTGTCGGTCAA
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
------gtaatatgacctccatttt-ctcttgaaaacaa--attcaaatgttttccatcttcaatacttacttactttctatgcatttacgatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
| | || || |||| || |||| | ||| | | || ||| | ||||| | || || | | ||| | ||| ||||||| | ||||| ||||| || || | || || | ||| |||||||||| ||||| ||||||||||||||||| ||||| |||| ||| | ||| |
gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaa-ttgctgattttctctttcc-atgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 8
gtaatatgacctccattttctcttgaaaacaaattcaaatgttttccatcttcaat-acttacttactttctatgcatttac--gatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
| || | || | | | |||| || || | |||||| ||||||| ||| |||| || |||||||||| ||||| || | |||||||||||||| ||| ||||| | ||||||||||| || | | |
-------------------------------------------------gtacagtgacaaatctgtatcttatgttttaacttattcctgcagGCACACCTTTGCAACTATGTCCTTCATCGCTGAGACATTTATCTTTTTATACGTTGGAATGGACGCACTGGACCTGGAGAAATGGAGGTTGGCAGATAAG
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 8
gtaatatgacctccattttctcttgaaaacaaattcaaatgttttccatcttcaat-acttacttactttctatgcatttac--gatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
| || | || | | | |||| || || | |||||| ||||||| ||| |||| || |||||||||| ||||| || | |||||||||||||| ||| ||||| | ||||||||||| | | | |
-------------------------------------------------gtacagtgacaaatctgtatcttatgttttaacttattcctgcagGCACACCTTTGCAACTATGTCCTTCATCGCTGAGACATTTATCTTTTTATACGTTGGAATGGACGCACTGGACCTGGAGAAATGGAGGCTGGCAGATAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgttttccatcttcaatacttacttactttctatgcatttacgatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
tacttac putative branch site (score: 1)
aatactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatgacctccattttctcttgaaaacaaattcaaatgttttccatcttcaatacttacttactttctatgcatttacgatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT