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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacatctctcttactcacagttcgttacagaattctcctttttgctttcttgttataacatttttcgttttcttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG

Basic information

species Arabidopsis thaliana
transcript AT5G62460.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G62460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g36740.4 (Oryza sativa), 3'ss of exon 6
gtacgtacatctctcttactcacagttcgttacagaattctcctttttgctttcttgttataacatttttcgttttcttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG
                                                         | ||      ||||  |   |  ||   | |  | |||   | ||     |  | || ||||| ||| | || || || || |||||||||||||||||||||||  | ||||||| |||||||||||||
-------------------------------------------------------cttcattgtgcatttcactagttgctgatctttaacagttgtttcttt----tgagggctgctggatttttgctgccatgctatatcatggcttgggctattagTATCATGCAACGTCAAAGACAAAGACAG

upper sequence: AT5G62460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------------------------gtacg-tacatctctct-tactcacagttcgttacagaattctcctttttgctttcttgttataacatttttcgtttt-cttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG
                                                                          | | | ||   |||  |  | |   |||  ||     |  |||  || ||  ||  ||| |    |||| | | |||  ||  |  ||  | |     || | ||  |  |  | || ||||| ||| | || || || || |||||||||||||||||||||||  | ||||||| |||||||||||||
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctg-ttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG

upper sequence: AT5G62460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G118957_T05 (Zea mays), 3'ss of exon 2
gtacgtacatctctcttactcacagttcgttacagaattctcctttttgctttcttgttataacatttttcgttttcttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG
               |  |   |  | | || || |  ||   | |||  |||   | | |||  ||  | |  |    | |||||      |  |||| ||  |  |  |||||||||| ||| | || || || || || ||||||||||||||||||||  | || |||| |||||||||||||
-------------gttagcgatcgatacattgcatatctcctgtgttttttttggcgatgtaaagttaattgactctgctggtcttt-----ggcagCTATTTCTTTTGAGAGCCGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG

upper sequence: AT5G62460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 5
gtacgtacatctctcttactcac-agttcgttacagaattctcctttttgctttcttgttataacatttttcgttttcttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG
               ||| | |  | | | ||  | |  ||   | |||  ||| | | | |||  ||    |  |   || || ||      |  |||| ||  |  |  |||| ||||| ||| | || || || || || ||||||||||||||||||||  | || |||| |||||||||||||
--------------gttagtgattaatacattgtatatctcctgtgttt-ttttgtcgatgtaaagttaactgactctgttggtattt-----gacagCTATTTCTTTTGAGAGCGGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG

upper sequence: AT5G62460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 6
-----------gtacgtacatctctcttactcacagttcgt-------tacagaattctcctttt-tgctttcttgttataacatttttcgtttt--cttttgtcttctttcggtt-------agCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG
            |  ||||   ||  ||  | | | || ||       ||      | | ||| | |   | | || |   |      | ||||   | ||    | | |  || |       |||||||| |||||||||| |||||||| || ||||| || ||||| ||||| |||||||| |||||||| || ||||||||||||||||||
gtgagtgagatatgtgtactattcatttgataataatttgtgtgcttgtatgtgtctatacttgtatatatccatggttgcatggaagtggtttcaccattaaaatacatatggatgcttgacagCTTTTCCTGCTTCGAGCTGCTGGTTTCCTTCTCCCTTGCTACATTATGGCCTGGGCTATCAGTATATTGCAGCGTCGAAGACAAAGACAG

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|47829320|gb|CK119004.1|CK119004
EST:     CAAACAACAACTCAGATGACGAAGAAGACGATCCATCAGCTTTCTTCTTT                         CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCT
genomic: CAAACAACAACTCAGATGACGAAGAAGACGATCCATCAGCTTTCTTCTTTgtacgtacat ... tttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCT
EST: gi|125307908|gb|EL321993.1|EL321993
EST:     CAAACAACAACTCAGATGACGAAGAAGACGATCCATCAGCTTTCTTCTTT                         CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGG
genomic: CAAACAACAACTCAGATGACGAAGAAGACGATCCATCAGCTTTCTTCTTTgtacgtacat ... tttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGG
EST: gi|125258078|gb|EL272163.1|EL272163
EST:     GCTTTCTTCTTT                         CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCT
genomic: GCTTTCTTCTTTgtacgtacat ... tttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttgctttcttgttataacatttttcgttttcttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG
               ttataac  putative branch site (score: 2)
                       tttttcgttttctttt  CT-rich tract
            ttgttataacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacatctctcttactcacagttcgttacagaattctcctttttgctttcttgttataacatttttcgttttcttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA