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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattgttttcctgtcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC

Basic information

species Zea mays
transcript GRMZM2G089630_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 5
----agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattgttttcctgtcacatgt-tttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
     |||  ||||  || ||| | |    || |  |      | | |  || | |    ||||   | || |   |||   | |  ||| |   | | ||  ||||||| ||| |  ||||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||| || || |||||||||||||| ||||| |
tggaggatatattt--tttataatctgttgttgccatgaccattactatttttatcg---tggcagggcctaacattttctttttttcatctacctgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAATTCATATGCATCGGAAGATTTACAGCAGTCTCGTTCCAAGTTCTAGGCC

upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
agatccatttgcttgatattataaattttcttt-ctttgctgcaagcttgac-caacctggccaagacttattgttttcctgtcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
  |||       |  | |    |  ||  |||  ||||     |  | | ||   | |   |   |||| ||  |||     ||||    ||   ||| |||||||| || || |||||||||| ||||||||| |||||||| |||||||||||||||||||| ||||||||||| || ||||| || ||||| ||||| |
-tatcatagcagtgcagacctgatgttcccttgacttttacatattccttacatgagcaaactgggactaatgctttcttcttcactcacttaa-tttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC

upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G31940.1 (Glycine max), 3'ss of exon 6
agatccatttgcttgatattataaattttcttt-ctttgctgcaagcttgac--caacctggccaagacttattgttttcctgtcacatgttttcctttt-cagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
  |  ||||| ||    ||| | ||||   | | | | |      || | |    ||| |  | |        | ||   ||        | |||  ||| ||||| || ||| |  | || ||||  || || || ||||| ||||| ||||||||||| ||||| || || |||||||| || || ||||||||||| || |
gaaatcattttct----attttgaattccatatgcataggcctttgcctaatgttaactttacaatagtactatattgaactaatctgcttcttctgtttgcagTTGTTCATCATTATCTCTTGCACCATCGCAGTAGGGACAAACCTCAGCCAGTTCATCTGCATTGGCAGGTTCACGGCTGTATCTTTCCAAGTCCTTGGAC

upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G15280.2 (Glycine max), 3'ss of exon 5
agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggcc----aagacttattgttttcctgtcacatgttttcctttt-cagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
      ||        |||  |  |  ||   ||       |||   |||  |   || |      |    |||| ||   |||         | |  | | ||||| || ||| |  |||| ||||  || || || ||||| ||||| ||||||||||| ||||| || || |||||||| ||  ||||||||||||| ||||
-----tataaatactgtatagtttacctttactcaagaaaacaataatgaatactgtgactcctggaatactattattaaactgagctgctcctgctgtctgcagTTGTTCATCATTCTGTCTTGCACTATCGCAGTAGGGACAAACCTCAGCCAGTTCATCTGCATTGGTAGGTTCACGGCTGTAACGTTCCAAGTCCTTGGTC

upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
agatccatttgcttgatattataaattttctttctttgctgca--agcttgaccaacctggccaa-gacttattgttt---tcctgtcacatgtt--ttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
      |   |  |||  |||| |  ||| ||   ||     |   | |||  || |    | || || || || |||   | |  | || || |  |   | | ||| | |||||     | ||||||| ||| ||  ||||||| ||||| ||||||||||| |||||||| |||||||| || || || ||||||||||| || |
------agaagggtga--ttatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgttctttgtattcaataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC

upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattg-----ttttcctgtcacatgttttc---cttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
        ||  || |  ||| |||   | | ||| ||||  | ||   |||   |||  ||    |  | |     | |||    |  ||||        | | ||| | |||||     ||||||||| ||| ||  | || |||||||||||||||||||| ||||||||||||||||| || || ||||||||||| || || |
-------cttagttaac-ttacaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatggtagaaacttattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC

upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 3'ss of exon 4
agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattgttttcctgtcacat-gtttt--ccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
 | |  |||| ||  |  | |     || ||  | |||   |  |||  |     ||   ||||| | ||   |  | || | | | || ||  | ||| ||| | |||||  |  | || || |  || || || ||||||||||| ||||||||||||||||| || |||||||| || ||||| || ||||| || || |
-ggtgaatttcctctagttcactttattcctagcattgtgccttgct--atttgtctttacaagaatgatctctcacttgcctcgttgtcttggcttttgcagATATTTATAATCCTTTCATGTACTATCGCGGTAGGGACCAACCTCAGCCAGTTCATATGCATTGGTAGATTCACAGCTGTCTCCTTTCAAGTACTTGGCC

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|93012953|gb|EB638473.1|EB638473
EST:     GGCTGACCAACAAAAGAGTCGATGCTTTTTACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCACCCTAAGC-AG
genomic: GGCTGACCAACAAAAGAGTCGATGCTTTTAACTACACATCAATAGTTACGgtatgtcata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAG
EST: gi|8382969|gb|BE056017.1|BE056017
EST:     GGCTGACCAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAG
genomic: GGCTGACCAACAAAAGAGTCGATGCTTTTAACTACACATCAATAGTTACGgtatgtcata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 41

TCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTTTTGTGGACTTCTGGCTGACCAACAAAAGAGTCGATGCTTTTAACTACACATCAATAGTTACGgtatgtcata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 60

TCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTTTTGTGGACTTCTGGCTGACCAACAAAAGAGTCGATGCTTTTAACTACACATCAATAGTTACGgtatgtcata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 52

TCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTTTTGTGGACTTCTGGCTGACCAACAAAAGAGTCGATGCTTTTAACTACACATCAATAGTTACGgtatgtcata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 68

TCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTTTTGTGGACTTCTGGCTGACCAACAAAAGAGTCGATGCTTTTAACTACACATCAATAGTTACGgtatgtcata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaccaacctggccaagacttattgttttcctgtcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
 gcttgac  putative branch site (score: 68)
                                      catgttttccttttc  putative PPT
                     ttattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattgttttcctgtcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA