Sequence
atgc intronic sequence ATGC exonic sequencegttcaactcttttgccattttgaccactctaaatgcttgcaatactctgtgaaagcaccaatctatttgtatctcttggctttcctcattttttttctgatgcagGATTCCCCTGTTTGGTGAATTCACCTGCCAAAATGCTATCTTGGCCGAGCGGTTCATTGAAGGAGGTAGCCC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52510.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52510.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g55180.1 (Oryza sativa), 3'ss of exon 6
gttcaactcttttgccattttgaccactctaaatgcttgcaatactctgtgaaagcaccaatctatttgtatctcttggctttcctcatttttt-ttctgatgcagGATTCCCCTGTTTGGTGAATTCACCTGCCAAAATGCTATCTTGGCCGAGCGGTTCATTGAAGGAGGTAGCCC
| |||| |||| || | | | | |||| | || | | | ||| ||||||||| | ||| | || ||||||| | || || ||||||||||| ||||||||||||||| | ||||| ||| | |||||||||| |||||||||
gctcaatattttt--cactaatgctgcagttgatgccatcttgccttttttgc--ccttaat--atttgtatcatggaagtaaattcaagtcacatttcaatgcagGTTGCCACTTTTTGGTGAATTTACCTGCCAAAATGCTGTTTTGGCTGAGAGATTCATTGAAGCAGGTAGCCC
upper sequence: AT1G52510.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G117531_T04 (Zea mays), 3'ss of exon 6
gttcaactcttttgccattttgac-cactctaaatgc-ttgca--atactctgtgaaagcaccaatctatttgtatctcttggctttcctcattttttttctgatgcagGATTCCCCTGTTTGGTGAATTCACCTGCCAAAATGCTATCTTGGCCGAGCGGTTCATTGAAGGAGGTAGCCC
|||||| | |||| || | ||| ||| | | || | | || | | | || ||| | || |||| |||||| || || ||||||||||| || || ||||||||| | ||||| ||||| |||||||||| ||||||| |
---------ctttgcccctctgacacagattgcatgtgcagcaggacaatcaaccctaccctatatgagtatatgactacacgctaacaatgcttcatttccaatgcagATGGCCACTCTTTGGTGAATTTACTTGTCAAAATGCTGTTTTGGCTGAGCGTTTCATTGAAGCAGGTAGCGC
upper sequence: AT1G52510.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 6
gttcaactcttttgccattttgacc-actctaaatgcttgcaatactctgtgaaagcaccaatctatttgtatctcttggctttcctcattttttttctgatgcagGATTCCCCTGTTTGGTGAATTCACCTGCCAAAATGCTATCTTGGCCGAGCGGTTCATTGAAGGAGGTAGCCC
| || | | ||||| | | | | ||| | || | | | | | ||||| | | ||| | | | | |||| || || ||||| || | ||||||||| ||| |||| |||||||| | || |||||||| |||||||||||||||||
-cttaatttaatgatgcttttgtcttatacaacatgttggctgcttgatcttgattc-ttattctatattaactactttgatgccttttcttttctttc----tagAATTCCTCTATATGGTGAATTTACCAGCCAGAATGCTATTATTGCTGAGCGGTTTATTGAAGGAGGTAGCCCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|124827081|gb|EH911947.1|EH911947EST: AGTCCGCTGACCGTTTCATCCCCAGTTCCCGGATTATTTAAGCAGCTGAG GATTCCCCTGTTTGGTGAATTCACCTGCCAAAATGCTA
genomic: AGTCCGCTGACCGTTTCATCCCCAGTTCCCGGATTATTTAAGCAGCTGAGgttcaactct ... tctgatgcagGATTCCCCTGTTTGGTGAATTCACCTGCCAAAATGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaagcaccaatctatttgtatctcttggctttcctcattttttttctgatgcagGATTCCCCTGTTTGGTGAATTCACCTGCCAAAATGCTATCTTGGCCGAGCGGTTCATTGAAGGAGGTAGCCC
ttctgat putative branch site (score: 3)
tatctcttggctttcc CT-rich tract
attttttttctgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcaactcttttgccattttgaccactctaaatgcttgcaatactctgtgaaagcaccaatctatttgtatctcttggctttcctcattttttttctgatgcagGATTCCCCTGTTTGGTGAATTCACCTGCCAAAATGCTATCTTGGCCGAGCGGTTCATTGAAGGAGGTAGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG