Sequence
atgc intronic sequence ATGC exonic sequence...tctgaaccaatctgaaattatgcaactcttactaccatttacgacttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtttatcagATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G45050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 4
tctgaaccaatctgaaattatgcaactcttactaccatttacgacttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtt---tatc---agATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG
|| | | |||| | | | | || || | | | | ||| || || || || |||| || || |||| |||| |||||| || ||||| || |||||||| |||||||| || | ||| ||||||||||||||| | || ||| | ||||||||||| ||||||
-ctctgtgattgtgaaccaaaagagagatgagatacagtttttatgcataaatataat----ggccattaagaataacagct-tgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG
upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 4
tctgaaccaatctgaaattatgcaactcttactaccatttacgacttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtt---tatc---agATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG-----------
|| | | |||| | | | | || || | | | | ||| || || || || |||| || || |||| |||| |||||| || ||||| || |||||||| |||||||| || | ||| ||||||||||||||| | || ||| | ||||||||||| ||||||
-ctctgtgattgtgaaccaaaagagagatgagatacagtttttatgcataaatataat----ggccattaagaataacagct-tgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGGTTATTATATA
upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 4
tctgaac-caatctgaaattatgcaactcttactaccat---ttacgacttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtttatcagATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG
|||| || | || || | | | | | |||| ||| | || | || ||| |||| | ||||| | || | |||||||||| |||||||| ||||||||||| ||||| |||| || ||||| ||||| || || || ||| | || ||||| || ||||||
atggaacgtaaacaatttttgtggagccttgatggatgtggattacagttta-ctgtatggtttgtgattaacaaattcct--gctgttactcttgtctg-cagATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG
upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
----tctgaaccaatctgaaattatgcaactcttactaccatttacgacttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtttatcagATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG
||| || | | ||| | | | | | | | | ||| || ||| ||| | | | || ||| | | ||||||| | |||||||| ||||||||||||||||| |||| || ||||||||||||| || || ||| |||| |||||| | | |||
aatcatagaatgaagaacactcgacgcagtcatgagggagagtggtg-cacgttaatgaaatgatgatttttcattctggga---tttatttttgttcaaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG
upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
------tctgaaccaatctgaaattatgcaactcttactaccatttacgacttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtttatcagATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG
|| ||| | | ||| ||| | |||| ||||| | | || || ||| | | || ||| ||| || | | | || | |||||||||| |||||||| ||||||||||||||||| |||| ||| ||||||||||||| || || ||| | || |||||| | | |||
acgagttcccaacttaacgaaaactat-ctctgtgtacttgaatttaacatgttgc-gtttaattaagactaattt--ctgcaaacttggct--tcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGMapped 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|164077679|gb|ES140883.1|ES140883EST: CCGGCACCTTCACATCCACATATTTACAGCAATGGACATATTTGTTTAG ATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAAT
genomic: CCGGCACCTTCACATCCACATATATACAGCAATGGACATATTTGTTTAGgtattgcttg ... ggtttatcagATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtttatcagATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG
ttatcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgaaccaatctgaaattatgcaactcttactaccatttacgacttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtttatcagATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - aaccaat
- - - - - -ctgaaat
- - - - - - - - - - - - - - - actacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - caataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaagc