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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagctgatttaaatatgattcttaatatagttgagattttaccgaacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG

Basic information

species Arabidopsis thaliana
transcript AT1G77440.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 3'ss of exon 4
-tgagctgatttaaatat--gattcttaatata-gttgagattttaccgaacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG
 |||    |  ||  | |    ||  ||  ||| | |||  |  | ||     | ||| ||  || |||    |    |  | | |  ||||   |  | |||||||  |||| ||||||||||| || || || |||||||||||||| ||||||||||| |||||  ||||||  || |||   |||
ttgatgatacctatcttttcactttgtaccatatgctgatttactgccttgttttatatttttaa-ggttcatactaatcaaaggtgattct---tgtaagcagGGAACTAGCGAAAGATTTTGTGGTTTCTGGCACTGCTTCAGAATCACTATATGGTGCTTGTGAGTCCATGTATAAGCCAAGCATG

upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g43570.1 (Oryza sativa), 3'ss of exon 5
tgagctgatttaaatatg-attcttaatatagttga---gattttaccgaacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG
     || | ||| |  |  | | | ||||   |||   |   ||      | || |  |   | |  || |      |||| | |  || | |||   ||||||||  ||||||| ||||| ||||| ||||| || || || || |||||||||||||| |||||  |||||| ||||||| | |||
--ttttggtctaagtccgtgtgcctgatatgtctgattaggcgtttgaacgcttgtttctcatattcttgtgagctgattgaggatgtttatttctg--tgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATATGGTGCTTGTGAGTCCATGTACAAACCAAACATG

upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G045371_T02 (Zea mays), 3'ss of exon 4
tgagctgatttaaatat-gattcttaatatagttgagattttaccgaacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG
|      | ||  |||| | || ||    |   |    |||||  |    |  |  |  |  |  |     |   |   |     | || |   | ||||||||| | || || ||||||||||| || ||||| || ||||||||| | |||||||| |||||| |||||| ||| || || |||
tatttatagttggatattgcttgttccagttcctagtgttttagtgcttgtagtcatgacctttatttatttaaatgatcatccatgctttacta-tgcagGGAGCTGGCCAAGGATTTTGTTGTTTCTGGAACAGCATCAGAATCTTTGTATGGTGCTTGTGAATCCATGTACAAGCCGGACATG

upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G117544_T02 (Zea mays), 3'ss of exon 3
------tgagctgatttaaatatgattcttaatatagttgagattttaccgaacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG
      | |||   || ||||  | | ||||       |      || ||  |     |   | |  || | | | |  |       ||  | |      || ||||||  |||| ||||||||||| ||||| || ||||||||||| || || |||||||| |||||  ||||||  || ||| | |||
taatgttaagcctgttgaaattcgttccttacatcctatactgacttgccatatggcctctctaccttg-taatcttatcagagtatttcctttt-----attcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG

upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G24270.2 (Glycine max), 3'ss of exon 3
tgagctgatttaaatatgattcttaatatagttgagattttac-cgaacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG
| |||   | |       |   | ||||   |  |  || ||      |||   || || |    ||   || | ||  |      | |   |  |||||||||| | || |||||||||||||| || || ||||| || || ||||| |||||||| ||||| || ||||| || || || |||
taagcaattcttccacctaaattaaataacctgtaagttgtatattgtcatatgagctggatgtatgta-attctttatcttactattttcttgtatgcagGGAGCTTGCAAAAGATTTTGTTGTTTCTGGCACTGCATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG

upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G10130.1 (Glycine max), 3'ss of exon 3
tgagctgatttaaatatgattcttaatatagttgagattttac-cgaacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG
  || | ||       | ||  | ||||   |  |  || ||      |||   || || |    ||   || | ||  |     || |   |   ||||||||| | || |||||||||||||| || || ||||| || || ||||| |||||||| ||||| || ||||| || || || |||
caagattatgcttcccttatagtaaataacctgtaagttgtatattgtcatatgagctggatgtatgta-attctttatcttacctttttcttgtttgcagGGAGCTTGCAAAAGATTTTGTTGTTTCTGGGACTGCATCTGAGTCTCTGTATGGTGCTTGTGAGGCGATGTTTAAGCCTGACATG

upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 4
tgagctgatttaaatatgattcttaatatagttgagattttaccgaacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaa-atgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG
|   ||||||  |   |||| |    | |  ||  |  |       |||| || || ||  |    |   | | || |   || ||||  || | || ||||||| | |||||||||||||||||  | || ||||| || || ||||| ||||||||||| || ||||||||||| || || |||
ttgtctgattataggttgatccaagctttctttttgggtgatattgacattatggt-gctttacctaattttctttaatttttcttcttcctcacatccagGGAGCTTGCTAAAGATTTTGTTGTTGCTGGTACTGCCTCTGAGTCTCTTTATGGTGCCTGCGAGGCCATGTTCAAGCCCGACATG

upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S138_33V6.1 (Physcomitrella patens), 3'ss of exon 5
---tgagctgatttaaatatgattcttaatatagttgagattttaccga-acatgatagttgcaatggtgagca-tgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG
   ||||    |  | ||    |  |||     |  |  ||| ||  |        |   | || |||||   | ||  ||      |  |   ||| || |||     || || || |||||||| ||||| |||||||||||||| ||| ||||||||||||| ||| | |||| |||||| ||| ||
agttgagacagtg-agatggcctctttatcgcggacgctattgtatggtcgttctgtgtcttcagtggtgtttactgaattattatgtaattgttctgaagGCA----ATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATATGGTGCCTGCGAATCTATGTACAAACCTGATTTG

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|86076869|gb|DR372626.1|DR372626
EST:     GGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA                         GGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATA
genomic: GGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAAgtatgctcgc ... ctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATA
EST: gi|116388094|gb|EG430686.1|EG430686
EST:     GGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA                         GGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATA
genomic: GGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAAgtatgctcgc ... ctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG
                                           ctctaaa  putative branch site (score: 3)
                                 cgcttgttctctct  CT-rich tract
                                            tctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagctgatttaaatatgattcttaatatagttgagattttaccgaacatgatagttgcaatggtgagcatgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC