Sequence
atgc intronic sequence ATGC exonic sequencegtaagtccaatcttatatacttgagtttcttttgacctcaaacttatttaaaacgtaaaaaaaaacagGTTTCTACACGACAAGGTCAAGCCACAAGTGGTGCACCGCGACATCCGAGCTAGCAACGTGCTACTTGATGAGGAGTTTGGAGCTCATTTAATGGGTGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52310.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g01410.1 (Oryza sativa), 3'ss of exon 3
------------------gtaagtccaa--tcttatatacttgagtttcttttgacctcaa---------acttattt---aaaacgtaaaaaaaaacagGTTTCTACACGACAAGGTCAAGCCACAAGTGGTGCACCGCGACATCCGAGCTAGCAACGTGCTACTTGATGAGGAGTTTGGAGCTCATTTAATGGGTGTT
|| | | ||| ||||| ||| |||| ||| | | | | ||| || | | | | ||| ||| | || |||||||| ||||| || || |||||||| || ||||| || ||||||||||||||||| ||||| ||||| | ||| | ||||| |||
taggccaaatgcgtatacgtcaatgcaagcccttatggcgttgtgttttgttttgctactattagttgctatttacttaccagtgctcattttgatccagATTTTTGCATGACAAGGTGAAGCCGCAGGTCGTGCACCGTGATATCCGTGCAAGCAACGTGCTACTTGACGAGGAATTTGGTTCCCATCTGATGGGGGTT
upper sequence: AT1G52310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G049895_T03 (Zea mays), 3'ss of exon 2
----------------------------gtaagtccaatcttatatacttgagtttcttttgacctcaaacttatttaaaacgtaaaaa-----aaaacagGTTTCTACACGACAAGGTCAAGCCACAAGTGGTGCACCGCGACATCCGAGCTAGCAACGTGCTACTTGATGAGGAGTTTGGAGCTCATTTAATGGGTGTT
||| | | | | || || || | | |||||||| | | || |||||| | ||||||||||| ||||| || ||||||||||| |||||||| || |||||||| ||||| || ||||| || || | ||| | ||||| ||
acctcctgatgtataatgactttcttatataaatattgcccactcacttcaagcagtgttcgatacctta-ttatttaaccactggtcattttcaatgcagGTTCTTGCACGACAAGGTAAAGCCGCAGGTGGTGCACCGTGACATCCGTGCAAGCAACGTCCTACTCGACGAGGATTTCGGGTCGCATCTGATGGGGGTG
upper sequence: AT1G52310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G08380.1 (Glycine max), 3'ss of exon 4
--------------------gtaagtccaatcttatatacttgagtttctt-ttgacctcaaacttatttaaaacgtaa-----------aaaaaaacagGTTTCTACACGACAAGGTCAAGCCACAAGTGGTGCACCGCGACATCCGAGCTAGCAACGTGCTACTTGATGAGGAGTTTGGAGCTCATTTAATGGGTGTT
| | | || | | ||| |||| || || | | || ||||| || | ||||||||||| ||||||||||| ||||||||||| ||||| || || || || |||||||| || || || ||||||||||||||||| || | |||||||||
atgactataattttcattccctcaaacaaaagtatttcccttatgtttgttgttaatggatatattgcttaaagtatactctttttcctcattttaacagGTTTCTGCACGACAAGGTTAAGCCACAAGTTGTGCATCGAGATATACGTGCTAGCAATGTTCTGCTGGATGAGGAGTTTGGAGCACAGCTTATGGGTGTT
upper sequence: AT1G52310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G20020.1 (Glycine max), 3'ss of exon 3
--------------------------------gtaagtcca-atcttatatacttgagtttcttttgacctcaaacttatttaaaacgtaaaaaaaaacagGTTTCTACACGACAAGGTCAAGCCACAAGTGGTGCACCGCGACATCCGAGCTAGCAACGTGCTACTTGATGAGGAGTTTGGAGCTCATTTAATGGGTGTT
||| | | | | | | || | || | | || || ||| | | | || ||||||||| || |||||||| ||||||||||| ||||| || || || || |||||||||| || || |||||||| |||||||| | | ||||| |||
gttacaagctggagttcagttaccaaccaaaaataaataaacaaataaaaagattccatatccacagcattttaatgtacttatttcctcatttcaa-cagGTTTCTCCATGACAAGGTTAAGCCACAAGTTGTGCATCGAGATATACGCACTAGCAACGTACTGCTGGATGAGGAATTTGGAGCACGCCTTATGGGGGTTMapped 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|164089853|gb|ES022511.1|ES022511EST: GAACATGAGATTGAACATCGCCACAACTCTTGCTCAAGGAATCGC GTTTCTACACGAC
genomic: GAACATGAGATTGAACATCGCCACAACTCTTGCTCAAGGAATCGCgtaagtccaa ... aaaaaaacagGTTTCTACACGAC
EST:
gi|124911252|gb|EH985332.1|EH985332EST: GACTGGAACATGAGATTGAACATCGCCACAACTCTTGCTCAAGGAATCGC GTTTCTACACGACAAGGTCAAGCCACAAGTGGTGCA
genomic: GACTGGAACATGAGATTGAACATCGCCACAACTCTTGCTCAAGGAATCGCgtaagtccaa ... aaaaaaacagGTTTCTACACGACAAGGTCAAGCCACAAGTGGTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatacttgagtttcttttgacctcaaacttatttaaaacgtaaaaaaaaacagGTTTCTACACGACAAGGTCAAGCCACAAGTGGTGCACCGCGACATCCGAGCTAGCAACGTGCTACTTGATGAGGAGTTTGGAGCTCATTTAATGGGTGTT
ttttgac putative branch site (score: 3)
tcaaacttatttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtccaatcttatatacttgagtttcttttgacctcaaacttatttaaaacgtaaaaaaaaacagGTTTCTACACGACAAGGTCAAGCCACAAGTGGTGCACCGCGACATCCGAGCTAGCAACGTGCTACTTGATGAGGAGTTTGGAGCTCATTTAATGGGTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA