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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtttaggccacttgatctgtaatctatctatgtgatatgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT

Basic information

species Arabidopsis thaliana
transcript AT4G26430.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 4
gtatgtgtttaggccacttgatctgtaatctatctatgtgatatgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT
||  || |||        ||   ||   | |   ||  | || |  |    |||||     ||| ||   | | |||        |  |||| || || || || || |||||||||||||||||||| ||||| || ||||||||||| ||||| || |||||||| |
gttagtttttttcttgtgtgtgttgctttttccataaataatttttgttaagactt-----aacgttagtacgtttg-----atttaaagACTGTAGAGGCAGAGAGGATATCTGTTGATCATGTTGCCCATCTCAAACCATCTGATGGTGGCTCTGCGGCGACTCAAT

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
gtatgtgtttaggccacttgatctgtaatctatctatgtgatatgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT
||| || |||   ||  |   | |||   ||| |||| |  | |          |||   |||||||   ||| |||  ||       |||| || || ||||| || |||||||| || |||||||| ||||| || ||||||||||| || ||||| || |||||||
gtaagtatttc--cccttctgtttgt---ctaactatatattgt---------tttttcttaacatttgtatgcttgataaa------agACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 4
--------------------gtatgtgtttaggccacttgatctgtaatctatctatgtgatatgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT
                     |||   |||   |   || |       | | || ||    |     | | |  || |  |  |  | |  |  |  |       || |||| |||||||| ||| ||||||| |||||||||||||| |||||||||||||||||||| || |||||||| || || |
gttgggttttatgacttctgctatcccttttcacattttaaatcactgtttctcaattaattgattcacttggattcccttctctctccc-tcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 4
--------------------gtatgtgtttaggccacttgatctgtaatctatctatgtgat-atgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT
                     |||   |||   |   || |       | | |  ||    | ||     |||| |  |    |   | |     |||     || || |||| |||||||| ||| | ||||| |||||||||||||| |||||||||||||||||||| || |||||||| || || |
gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaattaattgattgacttggattcccttctatcctcctcctcttgctt-tgc-tgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtgtttaggccacttgatctgtaatctatctatgtgatatgagagtggactttcaataacattgc--aatgattgtaaacgcgtgca--gACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT
             | ||||| |||    | | | |   | ||||   |     |    | |    |  |  ||| ||| |       | ||  ||| || ||||| ||||| || || |||||||||||||| |||||||| |||||||||||||| || ||||| ||||| |
----------gttcgacttgctcttcttttttttttaatcatatttcacctatcaccaactggggtaactgaattattttttcttgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT

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|116443196|gb|EG485788.1|EG485788
EST:     TTGATGGAATTCCTCAGTCGATGTTCGTGCATACCAGCTACACAATTGAG                         ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCA
genomic: TTGATGGAATTCCTCAGTCGATTTTCGTGCATACCAGCTACACAATTGAGgtatgtgttt ... acgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCA
EST: gi|86080018|gb|DR375775.1|DR375775
EST:     TCGTGCATACCAGCTACACAATTGAG                         ACAGTTGAAGCTGAAAGAATATCTGTTGATCATG-TGCACATCTTAAGCCA
genomic: TCGTGCATACCAGCTACACAATTGAGgtatgtgttt ... acgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCA
EST: gi|124907261|gb|EH981341.1|EH981341
EST:     ATGGAATTCCTCAGTCGATTTTCGTGCATACCAGCTACACAATTGAG                         ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACA
genomic: ATGGAATTCCTCAGTCGATTTTCGTGCATACCAGCTACACAATTGAGgtatgtgttt ... acgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACA
EST: gi|116443197|gb|EG485789.1|EG485789
EST:     TTGATGGAATTCCTCAGTCGATGTTCGTGCATACCAGCTACACAATTGAG                         ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCA
genomic: TTGATGGAATTCCTCAGTCGATTTTCGTGCATACCAGCTACACAATTGAGgtatgtgttt ... acgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgatatgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT
                      caataac  putative branch site (score: 2)
                   tttcaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtttaggccacttgatctgtaatctatctatgtgatatgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC