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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttttgtttgctttgtaaactccattattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 7
tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttttgt-ttgctttgtaa--actccattattaac-attgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA
        |    || |||   || || | ||   | | |            | |||||  | |||   | |   ||   ||  | |  | | |   | |||||| |  || ||| ||||| ||||| || || ||||| |||||||| || || ||||| ||||| || || ||||| |||||||||||||| || || || |
----atggtatgctgtagagcaatttacctgttcatttttttccatggagacatttttgcatcgctgaatcactgcttatttgctgattacttttaatctccagGGTGGTGAAGATGACAACTTTGCTATCGTGTTTGCTGCTATGGGAGTGAATATGGAAACAGCCCAATTCTTCAAACGTGATTTTGAAGAGAACGGGTCAA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 7
tactcaacttctatgaagattgatatagcagtcagtctctcaat---tcctgtgtagttttgtttgctttgtaaactccattattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA
||||  |      | || ||| |||| |      || | | |||   | || |  |  | |   |      ||| | |   |  | |  ||       | |||| |  || ||| ||||| ||||| ||||| ||||| |||||||| || |||||||| |||||||| || ||||| |||||||||||||| ||||| || |
tactgtaag---gtcaacattcatatggagcattgtgtattaatgtatgctttacatgtctaaatatggcttaatcactgcttctgatttttgtaacctgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 7
tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttttgtttgctttgtaaa-ctccattattaacattgtgtttttc-----cagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA
   ||   |    | || ||| |||| |  |   || |    |||| ||| |  |||   |  |||  |||  ||   | | |     ||  ||| |      |||| |  || ||| ||||| ||||| ||||| ||||| |||||||| || |||||||| |||||||| || ||||| |||||||||||||| || || || |
--ttcctgtgaggtcaacatttatatggaggattgtgt----attcatgtatgctttacatgtcttaataaggcttagtcactggttctgattttattacctgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 7
tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttttgtttgctttgtaaactccat--tattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA
   |  | |||| |         | |     || || |   | ||    | ||  |   |    | |||||    |||  ||||  | ||| |||| |  ||||| | | |||||||||||| || || || ||||| |||||||| ||||||||||| ||||| || ||||| |||||||||||||| ||||||||||| |
ccgttcatttctgtcctaccctttgtccacttctgttttatatttttcttttatctgattaaaatatgtaattctcatattatttgccttgagtttat--agGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 7
tactcaacttctatgaag--attgatatagcagtcagtctctcaattcctgtgtagttttgtttgctttgtaaactccattattaacattgtgtttttccagGAT---CATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA
  || | | | | |      |||| | | |  |  |   | || ||    ||| |    |   ||  |  | |       | ||  | |  |  ||   ||||||   || || || ||||||||    |||||||||||||||||||| || |||||||||||||||   || ||||| |||||||| || ||||| || |   
-cctaagcatttgttcttttattggtttggttgataccttttctataagcgtggaaggct-cctgagtaatgataaaatgtgttggcgtgttccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGT---

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 6
tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttttgtttgctttgtaaactccattattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA-----------------------------
                                                                                                       |  || || ||||| |||   || ||||| || |||||||| || |||||||||||||||   || ||||| |||||||| |||||||||||||| |                             
------------------------------------------------------------------------------------------------------gcccggtgaagacaacttttgtatcgttttcgctgctatgggagTTAACATGGAGACAGCTACTTTCTTCAAACGTGATTTCGAAGAAAATGGATCTATGGAGAGAGTGACACTTTTTCTCAACTTG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttt-tgtttgctttgtaaactccattattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA
                                    |  |   || | || ||  || ||| || | |  | |||     || |   |  |   | |||||  | |||  || ||||| |||||||| || ||||||||||||||||| ||||||||||| || |||||||||||  | |||||||| |||||||||||||
---------------------------------gtacaattgttttccgtttatcttctgtctgttgttgagactg----atgagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 6
tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttt-tgtttgctttgtaaactccattattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA
                                    || |   || | || ||  || ||| || | |  | |||     || |   |  |   | |||||  | |||  || ||||| |||||||| || ||||||||||||||||| ||||||||||| || |||||||||||  | |||||||| |||||||||||||
---------------------------------gtacttttgttttccgtttatcttctgtctgttgttgagactg----atgagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGA

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|116471926|gb|EG514518.1|EG514518
EST:     AGGCTGGACTTGTGAAGCGGTTGGAAAAGACTGAGAACTTAATTCAGGAG                         GATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAAC
genomic: AGGCTGGACTTGTGAAGCGGTTGGAAAAGACTGAGAACTTAATTCAGGAGgtaaatcatt ... gtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAAC
EST: gi|116483049|gb|EG525641.1|EG525641
EST:     AGGCTGGACTTGTGAAGCGGTTGGAAAAGACTGAGAACTTAATTCAGGAG                         GATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAAC
genomic: AGGCTGGACTTGTGAAGCGGTTGGAAAAGACTGAGAACTTAATTCAGGAGgtaaatcatt ... gtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtgtagttttgtttgctttgtaaactccattattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA
                                 tattaac  putative branch site (score: 1)
                                            tgtttttcc  putative PPT
                               attattaacattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttttgtttgctttgtaaactccattattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- ctcaact
- - - - - - atgaaga
- - - - - - - - - - - - - - - - - - ctctcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaactc