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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactcctatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG

Basic information

species Zea mays
transcript GRMZM2G135283_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactc--------ctatagctcaaaggttctacctactg---tttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
         ||| |  |  || ||| | |||||||||| |  ||||||||| ||||||| | |||||        | || ||| |   |||| || |  ||    ||||||||||| ||||||||||| || |||  ||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||
---------tgagtttc--ttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------atctgcaaatgaatgacattttcccataaat-tcttagtaacattcagata-----tgatgctctagat-----actcctatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
                                                                     || |   ||| | || | ||||    |  || ||||   ||   |    ||     ||  |   |  ||     | |    | | | ||   | || |      |  ||||||||| || || |||||||||||    ||||||||||||||||||||||| || |||||| | ||||| || ||||  ||||| || || |||
gtacttttgaagtttgaacttccaccattcatttcatcttataatcaaatctatagtgtgtatatggctatttaataattattgtcttttttattttgatatcttttcaaagattgagtagaccttggggtcattaatgaaaaattatactcgtttaatattgctgctataactacgcagACTGATACCAAAAAGATATCTGCTGTCTCAATATTTTTTGAGACAATGCCATATAGATTGAACGAAAGTACGGGATACATTGACTATGACCAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactcctatagc-----tcaaaggttctacctactgtt-tgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
     |||     |  || ||     | ||||| | ||||||  |       || | ||    |     ||        || ||  ||    |||||  | |||||||||| || || ||||||||||||   || |||||||||||||||||||| ||  ||||| ||||||| || ||||  || || || || |||
----acaagctc-tatcagttgtattttaattcat-gtaacaagctctctcaattcacttagcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 6
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactcc----tatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
    ||   | | |  ||  | ||| |  |    |  |||  |  ||  ||| ||  | | || ||       |    |   |   | |   |      ||||||||||||| ||||||||||| ||    || ||||| ||||| |||||||| ||||||||| |||| |||||||| |  || ||||| || |||
---agcctttcattagcaactccccttgcacctcttttaaattgtagcaatg-tgtgccatattctttgtaacaagattttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 6
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatg-atgctctagatactcctatagctcaaaggtt--ctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
     | | | | |  || || ||| |  | ||||  | |  |  ||  |||  |||  ||     |   | |  |    | ||   |   |      ||||||||||||| ||||||||||| ||    || ||||||||||| |||||||| ||||||||| |||| |||||||| |  || ||||| || |||
---aaccattcattagcaattccccttgcactcttttttaactgtagcaatgtgtgccatattctttgtaacaagtttttgattatttgtttgtgtcatgcagACTGACACCAAGAAGATATCAGCTGTATCTATATTTTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 6
----------------atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactcctatagctcaaaggttctacctactgtt-tgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
                 |||  |  |   | |  |       | | ||  |  |  |||     | ||    |     |    || |  ||||    || ||  | || || ||||||||||||| ||||| ||||| ||    || || ||||||||||||||||| |||||||||||||| | |||||| |  |||||||| || |||
gtacttgggttctagtctctctagcttggtca-gtcagtatttgactttcttttctcatctctttgtggaattgatattgtatcttttcctcatttcttttatttgctcttgtgcagACTGACACGAAGAAAATATCGGCTGTATCCATCTTTTTTGAGACAATGCCATACAGATTGGATGAGAACACTGGTTACATTGATTATGACCAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 3'ss of exon 6
-atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactcctatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG-------
    | | |||   |||   | || | |   ||  | |||  |||    |    |  | |           || |       ||    |     | ||||||| ||||| ||||| |||||||||   || |||||||||||||||||||| || |||||| |||| |||||||| |  ||||| || || |||       
aggtttctaatatttgatgatctctccttg-tttgtggtattattactttgccttcttatgtgctagggagtaacctcctcatttcttcgctattgtgcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAGGTAACTT

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 6
--atctgcaaatgaatgacattttcccataaattct-tagtaacattcagatatgatgctctagatactcctatagctcaaaggttctac-ctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
   |||   | |  ||||  | | |   |   |  | |  | || ||    | | |||  ||||  ||    |   |||     |||| | ||| |||  |||||| ||||| ||||| |||||||||   || |||||||||||||||||||| || |||||| |||| |||||||| |  ||||| || || |||
gtttctaatatttgatgatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaac--ctcctcatttcttcgctattgt--gcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
--atctgcaaatgaatgacattttcccataaattct-tagtaacattcagatatgatgctctagatactcctatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
   |||   | |  | ||  | | |   |   |  | |  | || ||    | | |||  ||||  ||    |   |   |    | | | || |||  |||||||||||| ||||| |||||||||   || |||||||||||||||||||| || |||||| |||| |||||||| |  ||||| || || |||
gtttctaatatttgaggatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttctttgc-tattgt--gcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
atctgcaaatgaatgacattttcccataaattctt--agtaacattcagatatgatgctctagatactcctatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
|| ||   |  |||  | | ||||  |   || ||    ||| |    |   | |   ||| |||  | |||    |  |   ||||    ||  ||||||||| ||||| ||||||||||||||    || |||||||||||||||||||| ||||||||||||||||  |||||||  ||||| || || |||
atttgaggaataatttcttcttcctttttttttttttgataaaagcttgtcttcagtatct-gatg-tgctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG

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|21987802|gb|BQ779330.1|BQ779330
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACA
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACA
EST: gi|211349901|gb|FL349172.1|FL349172
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|148973319|gb|EE024404.2|EE024404
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|149012532|gb|EE042603.2|EE042603
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATANNNNNNNGAGACAATGCC
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTT-GAGACAATGCC
EST: gi|148946029|gb|EC891328.2|EC891328
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|149048905|gb|EE048404.2|EE048404
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|148958252|gb|EC904466.2|EC904466
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|211286148|gb|FL173729.1|FL173729
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACA-TGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|60351519|gb|DN218492.1|DN218492
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|71299012|gb|DR785498.1|DR785498
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|148930308|gb|EE284699.2|EE284699
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|60346600|gb|DN213573.1|DN213573
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|67024112|gb|CO452861.1|CO452861
EST:     GGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGAT-TCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: GGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|148969981|gb|EE020895.2|EE020895
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|149081312|gb|EE170425.2|EE170425
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|148947246|gb|EC892606.2|EC892606
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|149089957|gb|EE179246.2|EE179246
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|148945831|gb|EC891120.2|EC891120
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT

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: 357

GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 313

GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 539

GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG