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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttacttctgacctttctctatctattgttcttgttaaaattgttttacttatccatttttgactctggtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG

Basic information

species Arabidopsis thaliana
transcript AT5G26360.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------gttttactt-ctgacctttctctatctattgttcttgttaaaattgtt--ttacttatccatttttgactctggtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG
                                                       || | |  |  | |  |  |  ||| |  || |  |||   ||||  |  ||| |    | || ||| | ||  |  | |||||| ||||||||| | |||||||| || |||||||||||||||||||| ||||| ||||| |||||| |||
gtatgtggaacgttagatgttttctctctgttgagtactactgatgaaattattagtctgatgtgttaaattgccaatattttctgctaatgtatgaattagtacttaatctaactttcttgtcactctt--tggcagTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTCATTGTTTTAG

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 3'ss of exon 4
-------------------gttttacttctgacctttctctatctattgttcttg----ttaaaattgttttacttatccatttttgactctggtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG
                     |  || |    |  || |||      | |||| |    | |    ||| || || || | ||| ||| |   ||   ||||||| ||||||||| | ||||| || || ||||||||||| || ||||| || || |||||||||||||| |
aatgaaactgcacgtagctcctaaaccttgagctcttttcttagccctattctcgatgctcagtcctgtattcctaatac-tttatgagtt--gtccatgcagTCTATGATTGAGCTAAGCCGCACACAGGATGAAGAAGTAGGAGATGGCACGACATCTGTTATTGTTCTTG

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 4
-----------------gttttacttctgacct--ttctctatctattgttcttgttaaaattgttttacttatccatttttgactctggtgat---tgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG
                     || || ||  ||  |   |  ||||| |||| ||||   |  ||   |  ||   | || ||  | || | |    ||||||| ||||||||  | || ||||| ||||||||||||||||||||||| || || ||||| ||||||||||
acccgtatatataccctaccatatttgtgtgctaatgtgcagtctatggttcatgttgtga--gtcccatgtacttaattgtggttgtgtttaaatgtgcagTCTATGATTGAACTAAGTCGTACACAAGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G069765_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------------------------gttttacttctg-acctttctctatctattgttcttgttaaaatt----gttttacttatccatttttgactctggtgat-tgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG
                                                                                                               |  | |  ||||   | ||| |   || ||  || |  ||    ||   |  || | | || ||  | || | || ||||||| ||||| ||  | || ||||| || |||||||||||||||||||| || || ||||| ||||||||||
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtgcagt-ctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------------------------gttttacttctg-acctttctctatctattgttcttgttaaaatt----gttttacttatccatttttgactctggtgat-tgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG------------------------------
                                                                                                               |  | |  ||||   | ||| |   || ||  || |  ||    ||   |  || | | || ||  | || | || ||||||| ||||| ||  | || ||||| || |||||||||||||||||||| || || ||||| ||||||||||                              
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtgcagt-ctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------------------------------gttttacttctgacctttctctatctattgttcttgttaaaattgttttacttatccatttttgactctggtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG
                                                                                    ||||   | |||  |||  | | |  ||||    | |      |  | | || |    | ||    |   ||| |  ||||||||||||||| | ||||| || |||||||| ||||| || ||||| ||||| ||||| |||||||| |
gtatgatctctttctttctgtgccccgctggttcttaatatgacatctttttttaattgtactcttttattttgcttttaggttgtttggttactgctcttgttatgtg-attgcctatatgttttctactcttctaacatgtgttctttttgagtggtgacagTCAATGATTGAGCTAAGCCGCACACAAGATGAGGAAGTAGGAGATGGAACAACATCTGTAATTGTTCTTG

Mapped 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|47829135|gb|CK118819.1|CK118819
EST:     ATGGGAATGCTATTCTTCGTGAGCTAGATGTCGCTCATCCTGCAGCTAAG                         TCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACA
genomic: ATGGGAATGCTATTCTTCGTGAGCTAGATGTCGCTCATCCTGCAGCTAAGgttttacttc ... gtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACA
EST: gi|164183977|gb|ES081932.1|ES081932
EST:     TGCTATTCTTCGTGAGCTAGATGTCGCTCATCCTGCAGCTAAG                         TCAATGATTGAGTTGAGCCGTACGCAAGNTGAAGAAGTTGGTGA
genomic: TGCTATTCTTCGTGAGCTAGATGTCGCTCATCCTGCAGCTAAGgttttacttc ... gtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGA
EST: gi|86074170|gb|DR369927.1|DR369927
EST:     ATGGGAATGCTATTCTTCGTGAGCTAGATGTCGCTCATCCTGCAGCTAAG                         TCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACA
genomic: ATGGGAATGCTATTCTTCGTGAGCTAGATGTCGCTCATCCTGCAGCTAAGgttttacttc ... gtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACA
EST: gi|47830309|gb|CK119993.1|CK119993
EST:     ATGGGAATGCTATTCTTCGTGAGCTAGATGTCGCTCATCCTGCAGCTAAG                         TCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACA
genomic: ATGGGAATGCTATTCTTCGTGAGCTAGATGTCGCTCATCCTGCAGCTAAGgttttacttc ... gtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgttcttgttaaaattgttttacttatccatttttgactctggtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG
                                  ttttgac  putative branch site (score: 3)
           ttaaaattgttttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttacttctgacctttctctatctattgttcttgttaaaattgttttacttatccatttttgactctggtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT