Sequence
atgc intronic sequence ATGC exonic sequencegtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35950.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 1
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
|| | | | | || | | |||||| || | | | | || || | ||| | ||| |||| || | | | | || || ||| | | || |||||||||| || ||||||||||| || || || |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||| |
----------attgtgtttcatgctatatatgatatta---tcttataaatatgtttat-tgataaa-gaaaaatgatcattattt-ttgcatctctt---cac-tttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 1
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaa-cagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
||| | || | | |||| |||| || || | | | ||| ||| | || ||| || | | | | | || || |||||| |||||||||| || ||||||||||| || || || |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||| |
------------aattgtgtttcaatgct---atatatgat--atcctcttataaatatgct---tattgagaaagaaagata-attttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatt-tccatt--ggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
| ||| ||| ||| || || | | || | |||| ||| || | ||| | | || ||||||| || | ||| ||||||||||||| ||||||||||| || || || ||||||||||||||||| ||||| || |||||||| || |||||||||||||| |
-----------------gtctcattttgtttattataaagtttggttaac---gttttttttttataaacattaggtta---acaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccata-tatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
| || || ||| | || || | | || |||| || | | ||| || | || | | | ||||||| | | | ||||||||||||| ||||||||||| || || || || |||||||||||||| ||||| || |||||||| || |||||||||||||| |
------------------tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactat---ttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccata-tatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG------------
| || || ||| | || || | | || |||| || | | ||| || | || | | | ||||||| | | | ||||||||||||| ||||||||||| || || || || |||||||||||||| ||||| || |||||||| || |||||||||||||| |
------------------tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactat---ttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
|| || ||| || | | | ||||| || | || | ||| || ||| || | || | | | ||| | ||||||||||||| || ||||||||||| || || ||||||||||||||||| ||||| ||||| || || ||||| |||||||||||||| |
------gaaaagaatcttccaaaaaaattaaggacttcggatcattc--ttttttttctttgataggcaaa---ggacttat-tgtttta-------tttttgaattattgg-gaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgatt-gtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
| |||| | || || | | | | | | || | ||| ||| |||||||||| ||||| |||||||| |||||||| || || ||||||||||| |||| ||| || || ||||| | ||||| ||||| |
-------------------------------------------gtgagatttcgttttgttctttcctttttctctaactctcttgggctgggatcgtt-----catc--------aacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGMapped 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|164050820|gb|ES009141.1|ES009141EST: TTGGTAAAACCTGTTTGCTGATTTCTTATACCAGCAACACCTT-CCCACG GATTATGTTCCGACTGTTTTCGATAACTTTAGTG
genomic: TTGGTAAAACCTGTTTGCTGATTTCTTATACCAGCAACACCTTTCCCACGgtattcatca ... attggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTG
EST:
gi|164079680|gb|ES009977.1|ES009977EST: TTGGTAAAACCTGTTTGCTGATTTCTTATACCAGCAACACCTTTCCCACG GATTATGTTCCGACTGTTTTCGATAACTTTAGTG
genomic: TTGGTAAAACCTGTTTGCTGATTTCTTATACCAGCAACACCTTTCCCACGgtattcatca ... attggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
tactaaa putative branch site (score: 1)
tttccatt putative PPT
atacatactaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG