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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggtctggtattagtcttggttagcagatagttctttaattttacctgcttctttgttacttgcatgtttgttggactaaacattaataatctccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG

Basic information

species Zea mays
transcript GRMZM2G451716_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 3
gtgagtggtctggtattagtcttggttagcagatagttctttaattttacctgcttctttgttacttgcatgtttgttggactaaacattaataatctccatt---ttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG
          |  | ||| |     ||  || |  |   ||||||||||| |   | ||  || ||  | |  ||| |  | ||  ||     |||   ||||   | ||||| ||  ||||||| || |||||||||||||||||||||||||||| |   ||| | | ||| ||| ||
---------ttccttttattgaacatttccacaatgaaatttaattttactttagtattcctttctctctt--ttgcttaattattcacatggaattaacattaattgcagAACAATGGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACTATTCTATCAG

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA04G37810.1 (Glycine max), 3'ss of exon 10
gtgagtggtctggtattagtc--ttggttagcagatagttctttaattttacctgcttctttgttacttgcatgtttgt-tggactaaacattaataatctcc-------atttt-----------cagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG
            ||||| | |  ||| ||   ||  |  | |||| ||  || ||||  ||  ||  ||   |  ||   || | ||| ||| ||||   | |       ||| |           ||||| || || |||||||| |||||||||||||| |||||| ||||||   | ||| |||||||  | |||
------------gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgattgattctttacttaaatgaagtaatcataaatatgtttctaagTCAATTCTACAAATGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAG

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 4
gtgagtggtctggtattagtcttggttagcagata-gttctttaattttacctgcttctttgttacttgca--tgtttgttggactaaacattaataatctccatt---ttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG
               ||  | ||  | | ||  |    | |  ||||| |  | |||   | || ||| |   | ||||||  | ||  ||     ||||  ||||   | ||||| || |||||||| || |||||||||||||||||||||||||||| |   ||| | ||||| ||| ||
--------------gttccttttattgaacatttccactatgaaatttaatttactttagtattcctttctcctttttgtttaattattcacatggaatcgacattaattgcagAACAAATGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACCATTCTATCAG

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 8
gtgagtggtctggtattagtcttggttagcagatagttctttaattttacctgcttctttgttacttgcatgtttgttggactaaacattaataatctccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG
|  |||  |    |||| |   | | |||  ||| | |  || | || |      |  |  | | |   |||||| |  | |  ||   ||  |||      || ||||| || || |||||||| |||||||||||||| |||||| ||||||   | ||| |||||||  | |||
gcaagtatt----tatttggacttgctagttgattgattctttacttaaatgaagtaatcataaat---atgtttctaagtc--aattctacaaat----ggttgcagAACAAATGTAATGTTGGCTATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAG

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgagt-ggtctggtattagtcttggttagcagatagttctttaattttacctgcttctttgttacttgcatgtttgttggactaaacattaataatctccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG
||  |  || ||  ||   || ||  | | |  || |   | ||||    |||  |   ||      |   | |   | |   ||||      |    || |||| |||||||| |||||||| || ||||| ||||||||| | ||| | ||||| ||||||||||| |||||||||
gtatgcaggcctcttacctgttttt-tcatctaatggag-tctaatgcagccttatagcttagggtat-tttctacatcgatataaatgaaccttccttctatttgcagAATAAATGCAATGTCGGATATGCTTTCATCAACCTTATCGAACCTGAAAATATTGTTCCGTTTTATAAG

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S78_22V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------------------------------------------gtgagtggtctggtattagtcttggttagcagatagttctttaattttacctgcttctttgttacttgcatgtttgttggactaaacattaataatc-tccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG-------------------------------
                                                                              || | || | |          ||| |      | |           |    | || | | |     | | |  ||| ||     |  |      |  |   |   ||||| |||||||||||||| ||||| ||||||||||||||    ||       || ||||| ||||| |||                               
gtacgttgaccggcactgtgatgggttgagtatttggtagtggtcgggtggagcataggtgtgcattccaagtaggtttggggggacagaacgagacagtgggtgaggtgtggaggggggcacgtgtggggttgtgtttggtgcgaaggcgtgtgggtaacgaggtggcgcgtgatgggtgcgcagAACAAGTGCAATGTTGGGTATGCGTTCATCAACATGATGTCGCCGTCGCGCATAGTTCCGTTTTACAAGGCGTTCAACGGGAAGAAGTGGGAGAAGTTCA

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 12
lower sequence: EFJ29695 (Selaginella moellendorffii), 3'ss of exon 7
gtgagtggtctggtattagtcttggttagcagatagttctttaattttacctgcttctttgttacttgcatgtttgttggactaaacattaataatctc---cattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG
                                                      |  |||    |  |||    ||||   ||    ||| |    ||    | | | |||||||| ||||| ||||| ||||||||||||||||||| | | || |   | || || || ||||| |||
-----------------------------------------------------gtgattttaggcgagcaaaagtgtttccctgg-tattgaccggcttttgcctgtgcagAATAAATGCAACGTTGGCTATGCATTCATCAACATGACCGAGCCAGCTCACATCGTCCCCTTTTACAAG

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|78073984|gb|DV502418.1|DV502418
EST:     AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG                         AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
genomic: AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
EST: gi|5895966|gb|AW037212.1|AW037212
EST:     AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG                         AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
genomic: AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
EST: gi|5895962|gb|AW037208.1|AW037208
EST:     AAAGTCACCGGGGAATTTATGATTTTATCTACCTGCCAATTGACTTTAAG                         AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
genomic: AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
EST: gi|213191920|gb|FM183353.1|FM183353
EST:     AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG                         AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
genomic: AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
EST: gi|76928188|gb|DV171510.1|DV171510
EST:     AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG                         AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
genomic: AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
EST: gi|31358340|gb|CD442697.1|CD442697
EST:     AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG                         AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
genomic: AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
EST: gi|166548745|gb|EG283059.1|EG283059
EST:     ATTTTATCTACCTGCCAATTGACTTTAAG                         AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
genomic: ATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
EST: gi|71301676|gb|DR786905.1|DR786905
EST:     AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG                         AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
genomic: AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
EST: gi|91048864|gb|EB159282.1|EB159282
EST:     AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG                         AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT
genomic: AAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAAT

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: 46 (upstream exon), 49 (downstream exon)
Score: 385

GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 234

GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 129

GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAGgtgagtggtc ... ccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctttgttacttgcatgtttgttggactaaacattaataatctccattttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG
                                          tctccattttc  CT-rich tract
                           actaaacattaataat  TA-rich tract