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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctaccagattacatatatacatgcctaccgactccttgctgatggtttgttttattcgaggttgatgatttacccttgttttattttgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG

Basic information

species Zea mays
transcript GRMZM2G145107_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145107_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g58080.1 (Oryza sativa), 3'ss of exon 9
gtacgctaccagattacatatatacatgcctaccgactccttgctgatggtt------tgtttt---attcg-aggttgatgatttacccttgttttattttgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG
||| ||||||  |  |||| ||| ||||  || |  || | ||||||| ||       ||||||   ||| | || |||||| | | |     | |  ||| || ||||||||||| ||||||||||||||||||||||| ||||||||||||||||| || |||||||||||||| ||||||||  | |||||||| |||||||||||||
gtatgctaccttaagacatctatgcatgtatatcagctgcatgctgattgtctcttactgttttggaatttgtagattgatggtgttcatccatatcgttt-gctttgcagTTGTCGTGGTTTCCCTTTTTCCTTTTTGATACTGACTGGATGGGACGTGAGGTTTACCATGGGGACCCAAATGGCAACTTGAGTGAAAGGAAAGCTTATG

upper sequence: GRMZM2G145107_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G40980.1 (Glycine max), 3'ss of exon 9
----------------------------------------gtacgctaccagattacatatatacatgcctaccgactccttgctgatggtttgttttattcgaggt--tgatgatttacccttgttttattttgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG
                                         |  | |  || ||    | | |   ||  | |      | |  || ||||   |    || ||  |  |  | || | |||||   |  | |   | |||||||||| ||||||||||| || || ||||| || || ||||||||  | |||||||| ||||| |||||||| || ||      |||     |   |||||
gtatgtactagtatttatttgcaaaggtttctgctaatatttgtgttttcaaatcggttgtgt-tgtgaatgctattagcctagtgctggtgcttcccttttgaaatccttcttatgttccctttaatcctatctacctgcagTTGTCTTGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGGAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATG

upper sequence: GRMZM2G145107_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G15950.1 (Glycine max), 3'ss of exon 10
----------------------------------------gtacgctaccagattacatatatacatgcctaccgactccttgctgatggtttgttttattcgaggttgatgatttacccttgttttattttgcct---tgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG
                                         |  | |  ||  |    | | |   ||  | |      | |  || ||||   |   ||| ||  |   |  | |   | | ||  ||  || ||   |||||||||||||||||||||| || || ||||| || || ||||||||  | |||||||| ||||| |||||||| || |       |||     |   |||||
gtatgtactagtatttatttgcaaaggtttctgttgatatttgtgttttcaagtcggttgtgt-tgtgaatgctattagcctagtgttggtgcttcccatttgaaatccttcttatgttcat-ttcaatcctgtctacctgcagTTGTCATGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGCAGAGAAGTTTATCATGGTGATCCAAAAGGGGGCACTTCTGAAGTAGATCTTTATG

upper sequence: GRMZM2G145107_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT2G02860.2 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------gtacgctac--cagattacata-tatacatgcctaccgactccttgctgatggtttgttttattcgaggttgatg-atttacccttgttttattttgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG
                        |  | ||   || ||| || | | |   |        |||| ||  ||||  ||    ||||| |    || |  ||||    ||||  | || | | |||||||| || ||||| ||||| || || || || || || ||||||||| | ||||||||||||||||||||||  ||||||       | | | ||   ||||
gtgagtgccaaagaaaaattatgatcagttattacatatttcacactgtttcttttcttaaactctttaatgatctttaaaattatttgcttctgttatatttttgattgtggtcttgttctttgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGATAGTTTGCATATGGAACTCTATG

upper sequence: GRMZM2G145107_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv01s0026g01960.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------------------gtacgctaccagattacatatatacatgcctaccgactccttgctgatggtttgttttattcgaggttgat--------gatttacccttg---ttttattttgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG
                                                    |  || || |||  | ||   | ||  ||  || |  |      | || | | |   |   ||||| |        |  ||  |||||   || || |      ||||| |||| ||||||||||| || |||||||| || || ||||||||  | |||||||| ||||||||||| || || |||  |  ||     ||||| ||||
gtaagtgcctcagtagttacatgtcaccaattttgtttccaatactgcatggcaatatcaaatttgaaattagcttgtttattgattattgatcattagtgtttctgtgtaatggttgctctgttgaggtcttttccttgatattatactcctgtatgcagCTGTCCTGGTTTCCCTTCTTTCTTTTTGATACGGATTGGATGGGTAGAGAAGTTTATCATGGGGATCCTAAAGGGGATGAGTCTGCAGTTAAAGCATATG

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|28361756|gb|CB240112.1|CB240112
EST:     ATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGG                         TTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAA
genomic: ATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAA
EST: gi|89756976|gb|DY686775.1|DY686775
EST:     ATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGG                         TTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGGACGCGA
genomic: ATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGG-ACGCGA
EST: gi|29544421|gb|CB604801.1|CB604801
EST:     ATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGG                         TTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAA
genomic: ATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAA
EST: gi|29544547|gb|CB604927.1|CB604927
EST:     ATCTACCTCCTGGGATGCATTCAG-GCTTCTAGTTATGGCCCTAACATGG                         CTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAA
genomic: ATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAA
EST: gi|28361547|gb|CB239903.1|CB239903
EST:     TCTACCTCCTGGGATGCATCTCAG-GCTTCTAGTTATGGCCCTAACATGG                         TTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAA
genomic: TCTACCTCCTGGGATGCAT-TCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAA
EST: gi|19855127|gb|BQ060179.1|BQ060179
EST:     ATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGG                         TTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGG
genomic: ATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGG

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), 49 (downstream exon)
Score: 41

CAATGATGGGCCAGGAGCAGTTTTGGTTAACATTTTGACCAGAATGAGGCATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

CAATGATGGGCCAGGAGCAGTTTTGGTTAACATTTTGACCAGAATGAGGCATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

CAATGATGGGCCAGGAGCAGTTTTGGTTAACATTTTGACCAGAATGAGGCATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 64

CAATGATGGGCCAGGAGCAGTTTTGGTTAACATTTTGACCAGAATGAGGCATCTACCTCCTGGGATGCATTCAGTGCTTCTAGTTATGGCCCTAACATGGgtacgctacc ... tgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtttgttttattcgaggttgatgatttacccttgttttattttgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG
                               cccttgttttatttt  CT-rich tract
                                  ttgttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgctaccagattacatatatacatgcctaccgactccttgctgatggtttgttttattcgaggttgatgatttacccttgttttattttgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA