Sequence
atgc intronic sequence ATGC exonic sequence...gaatcggttgattccgcgttggttcagtaacctcgtctttgaatttctgatctgatctgatagttctcagtgatttgacattttcttttatgggatgcagGTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTATGAGTTAGTGCGTGTTGGTCATGATAATTTGATTGGTGAAATCATCCGTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78900.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 1
gaatcggttgattccgcgttggttcagtaacctcgtctttgaatttctgatctgat-ctgatagttctca---gtgatttgacattttcttttatgggatgcagGTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTATGAGTTAGTGCGTGTTGGTCATGATAATTTGATTGGTGAAATCATCCGTC
| | || ||| | || | | | | | ||| || | | || | | | ||| || | || || | | | ||||||||||| || || || ||||| ||||| ||||| ||||||||||||||||| | ||||||||||||||||||||| | ||||||||||| || ||||
--aacattttattt-acttttttcctatg-ttgaggatgtgatccacttaattaataccatttactttcatgtatgctaaattatgttttcccaattaaaacagGTTTCAGGACCCGTCGTCGTTGCGGATGGCATGGCTGGTGCTGCTATGTATGAACTCGTGCGTGTTGGTCATGATAATCTCATTGGTGAAATTATTCGTC
upper sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 1
gaatcggttgattccgcgttggttcagtaacctcgtctttgaatttctgatctgatctgatagttctcagtgatt----tgacattttcttttatgggatgcagGTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTATGAGTTAGTGCGTGTTGGTCATGATAATTTGATTGGTGAAATCATCCGTC
||| | | | ||| | | || | | || | || | | ||| ||| | | | |||| | | | || ||||| ||||| || || || ||||| ||||| ||||| || |||||||||||||| | ||||||||||||||||||||| | ||||||||||| || ||||
----tttttgctgttactgtaattcgttgagggtgtgatctacttagttccatgttttaataactcttcattctcctcctcacatatattcccaattgaaacagGTATCAGGACCAGTCGTCGTTGCAGATGGCATGGCTGGGGCTGCTATGTATGAACTCGTGCGTGTTGGTCATGATAATCTCATTGGTGAAATTATTCGTC
upper sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 1
--gaatcggttgattccgcgttggttcagtaacctcgtctttgaatttctgatctgatctgatagttctcagtgatttgacattttcttttatgggatgcagGTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTATGAGTTAGTGCGTGTTGGTCATGATAATTTGATTGGTGAAATCATCCGTC
|| || || | || | |||| | | | | | | | | | || || || | | | | ||| || ||||| || || || || || || || ||||| |||| || || ||||||||||||||||| ||||| || |||||||| |||||||| || || || || |
cagagtcacttcacagaattagggcttagta-catgattcctctgatgttaagtaaacatcatc-tttatggttactgattgatgtatttaattcttgtcagGTCTCCGGGCCAGTGGTGGTAGCTGATGGAATGGGAGGAGCAGCTATGTATGAGTTAGTTCGTGTGGGACATGATAAGTTGATTGGAGAGATAATTCGACMapped 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|116482299|gb|EG524891.1|EG524891EST: CGA-CTTCGAGGACGATGAGAAGGAGAGCGAGTATGGTTACGTTCGTAAG GTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTAT
genomic: CGACCTTCGAGGACGATGAGAAGGAGAGCGAGTATGGTTACGTTCGTAAGgtattatcct ... tgggatgcagGTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTAT
EST:
gi|116482298|gb|EG524890.1|EG524890EST: CGACCTTCGAGGACGATGAGAAGGAGAGCGAGTATGGTTACGTTCGTAAG GTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTAT
genomic: CGACCTTCGAGGACGATGAGAAGGAGAGCGAGTATGGTTACGTTCGTAAGgtattatcct ... tgggatgcagGTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgatctgatctgatagttctcagtgatttgacattttcttttatgggatgcagGTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTATGAGTTAGTGCGTGTTGGTCATGATAATTTGATTGGTGAAATCATCCGTC
ttttcttttat CT-rich tract
acattttcttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatcggttgattccgcgttggttcagtaacctcgtctttgaatttctgatctgatctgatagttctcagtgatttgacattttcttttatgggatgcagGTTTCAGGTCCTGTTGTTGTTGCCGATGGTATGGCCGGTGCTGCTATGTATGAGTTAGTGCGTGTTGGTCATGATAATTTGATTGGTGAAATCATCCGTC
- - - - - - - - - - - - cagtaac
- - - - - - - - - - - - - - - - - - - - - - - ctgatct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatttga