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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagatattgttgaattctaattcatgtcttgttacttgattcagatgttttgctttaggattctgatatttgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG

Basic information

species Arabidopsis thaliana
transcript AT1G02560.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g19510.1 (Oryza sativa), 3'ss of exon 4
----------------gtcagatattgttgaattcta-attcatgtcttgttacttgattcagatgttttgctttaggattctgatatttgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
                  | |||    | | |   || |||||||  ||  |||||   |    |  |    | | |  |||   |      |  |||     |||||||  | |||||||| ||||||||||| |||||||| |||||||
gatttcatctaccaggacctgattccatggcaccatatattcatgatttcgtacttacattcagtactcgattcttgacttcctctcaacattcctgt-----agGATATCATTATGTATGTGAATTCTCCTGGAGGATCAGTGACAGCTG

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G01510.2 (Glycine max), 3'ss of exon 4
-----gtcagatattgttgaattctaattcatgtcttg---ttacttgattcagatgttttgctttag---gattctgatatt-tgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
      |    | || ||   || |   ||||||  ||   | |     |||   ||  |    ||||     | |  || || || ||||||||  |||||||||||||||||||| |||||||| || || |||||||||||||
ttttgtttttttgtttttatcttttgtatcatgtgatgaattcaaaattttcttgtgcatgcacttagtcaactaccaattttctgattatgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCAGTTACAGCTG

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G01550.1 (Glycine max), 3'ss of exon 4
---gtcagatattgttgaat--tctaattcatgtcttgttacttga----ttcagatgttttgctttag---gattctgatatt-tgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
   ||   |  || ||| ||  | |   | ||||  ||  |||  |    |||   ||  |    ||||     | |  || || || ||||||||  |||||||||||||||||||| |||||||| || || || ||||||||||
aatgttgaaattttttgtatcgtttgtattatgtgatga-actcaaaattttcttgtgcatgcacttagtcaactaccaattttctgattatgttgggcagGATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTG

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G37880.1 (Glycine max), 3'ss of exon 3
gtcagatattgttgaattctaattcatgtcttgttacttgattcagatgtt--ttgctttaggattctgatatttgct---tatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
           |||| |  ||     ||| |  ||   |||     |||||  | |    |||| |     |  | ||   ||| |||  ||||||||||||||||| || | |||||| || ||||||||||||||||
----------tttgattattaccctgtgtatgctt---tgaactcaatgttggtagtgcaaggacttaatcaactactaattattttgttcaggatattgtcatgtacgtaagTTCTCCGGGAGGATCAGTTACAGCTG

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G40480.1 (Glycine max), 3'ss of exon 3
-------gtcagatattgttgaattctaattcatgtcttgttacttgattcagatgtt--ttgctttaggattctgatatttgct---tatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
        | |    ||||    ||  |  |  |    | |   ||||     || ||  | |    | || |     |  | ||   |||||||  ||||||||||||||||| || |||||||  || ||||||||| ||||||
tttgattattaccctttgtctgctttaatctttttgtgtatgctttgaactcaattttggtagtgcaaagacttaatcaactactaattatgttgttcagGATATTGTCATGTACGTAAATTCTCTGGGAGGATCAGTTGCAGCTG

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 3'ss of exon 4
---------------gtcagatattgttgaattctaattcatgtcttgttact-tgattcagatgttttgctttaggattctgatatttgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
                | |  |  | || ||       | |    |   |||  | || ||  | ||   | ||||     | || | |   |||  |||||||||||||||||||||||| || ||||| || ||||||||||||||||
tttttctatagctctctgactttctattaaacagcttatgaaaattaactaccattatgcaagttttcaccattaga----tcatgtcttgatattctgaacagGATATTGTCATGTATGTGAACTCTCCAGGAGGATCAGTTACAGCTG

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S49_191V6.1 (Physcomitrella patens), 3'ss of exon 4
gtcagat--attgttg-aattctaatt---catgtcttgttacttgatt-cagatgttttgctttag--gattctgatatttgcttatgttg---aacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
||| | |  ||  ||| || |||  ||   ||| | ||| | ||  ||    | | | || ||||     | || | |||||   |  |||      |||||||||||||||||||||||||| |||||||| || || ||||| |
gtctgttgcatccttgcaagtctggtttgacatctattgctgctctatcatgggtctcttcctttttctaactcagttatttctgtcggttttctggcagGATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ24258 (Selaginella moellendorffii), 3'ss of exon 3
gtcagatattgttgaattctaattcatgtcttgttacttgattcagatgttttgctttaggattctgatatttgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
                                |||  | | ||   |  | | |    | |||  | | |  |   |   ||    ||||||||||||||||||| ||||| ||||| || || ||||| ||||
--------------------------------gtttgtgggttataacatgtag----aagatggttaaagctcgattgattttgtagGATATTGTCATGTATGTAAATTCACCTGGAGGTTCCGTTACCGCTG

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ35520 (Selaginella moellendorffii), 3'ss of exon 3
gtcagatattgttgaattctaattcatgtcttgttacttgattcagatgttttgctttaggattctgatatttgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
                                |||  | | ||   ||    ||    ||     | |   | | ||   ||    ||||||||||||||||||| ||||| ||||| || || ||||| ||||
--------------------------------gtttgtgggtt---ataacatgtagaagatggttaaagctcgattggtttttgtagGATATTGTCATGTATGTAAATTCACCTGGAGGTTCCGTTACCGCTG

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|125010098|gb|EL082367.1|EL082367
EST:     AATTGTAGCTCAACTCCTGTATCTTGATGCTGTTGATCCTACTAAG                         GATATTGTCATGTATGTTAAT
genomic: AATTGTAGCTCAACTCCTGTATCTTGATGCTGTTGATCCTACTAAGgtcagatatt ... tgttgaacagGATATTGTCATGTATGTTAAT
EST: gi|125295501|gb|EL309586.1|EL309586
EST:     ACATAATTGTAGCTCAACTCCTGTATCTTGATGCTGTTGATCCTACTAAG                         GATATTGTCATGTATG
genomic: ACATAATTGTAGCTCAACTCCTGTATCTTGATGCTGTTGATCCTACTAAGgtcagatatt ... tgttgaacagGATATTGTCATGTATG
EST: gi|125289367|gb|EL303452.1|EL303452
EST:     ATCCTACTAAG                         GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
genomic: ATCCTACTAAGgtcagatatt ... tgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
EST: gi|125078993|gb|EL141169.1|EL141169
EST:     ACATAATTGTAGCTCAACTCCTGTATCTTGATGCTGTTGATCCTACTAAG                         GATATTGTCATGTATGTTAATTCTCCTGGTGGAT
genomic: ACATAATTGTAGCTCAACTCCTGTATCTTGATGCTGTTGATCCTACTAAGgtcagatatt ... tgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGAT
EST: gi|164035784|gb|ES198643.1|ES198643
EST:     CATAATTGTAGTCTCAACTCCTGTATCTTGATGCTGTTGATCCTACTAAG                         GATATTGTCATGTATGTTAATTCTCC
genomic: CATAATTGTAG-CTCAACTCCTGTATCTTGATGCTGTTGATCCTACTAAGgtcagatatt ... tgttgaacagGATATTGTCATGTATGTTAATTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttgattcagatgttttgctttaggattctgatatttgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG
                             ttctgat  putative branch site (score: 3)
                                tgatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagatattgttgaattctaattcatgtcttgttacttgattcagatgttttgctttaggattctgatatttgcttatgttgaacagGATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG