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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgatcacctttttgtttgctaaatcagatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctttgaaaattttgataaataatcatctagtatccttgatgcgaaacataattctatggttcttttggtaacctagtaatccacacgcttgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
gtaagctgatcacctttttgtttgctaaatcagatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctttgaaaattttgataaataatcatctagtatccttgatgcgaaac--ataattctatggttcttttggtaacctagtaatccacacgcttgttct--gcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG
                                            ||  | |  ||     |||   || ||   ||  ||  |||   || ||||  |  |||  |  ||     | ||||||| ||    |    |||||  | |  | ||     |  |  | |||     | ||||||        || ||||  |||||| ||||||||||||||||||||| |||||||  | ||||||||||| ||||||||||| ||||||
-------------------------------------------gtaagtgtgcatcgcattattgttagatgc-taagtaactatggttagatatgcagtttttga--ttcatgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 11
gtaagctgatcacctttttgtttgctaaatcagatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctttgaaaattttgataaataatcatctagtatccttg--atgcgaaacataattctatggttcttttggtaacctagtaatccacacgcttgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG
                                                                ||  | |  || |   |||||||     ||||||    | || | || |||  ||||| || | ||| |   |  || |       | || ||   |    |||  |   || || |      ||| |   ||||||||||||||||  |||||||||| || |||||||| || ||| |||| ||||||||||| || |||
---------------------------------------------------------------gtaagtttcaat-tgcgtatatattgccttatataa---taaacagttggat--ataattattttgtaccagagggatacattctccagttataatttcacattgagatgatattagtatttgtgct-gaattgcagATATTCTACTTCATTGGATTTGGCCTTTTCTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 10
gtaagctgatcacctttttgtttgctaaatcagatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctttgaaaattttgataaataatcatctagtatccttgatgcgaaacataattctatggttcttttggtaacctagtaatccacacgcttgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG
                                        ||  |||   | | |  |  ||| |||  || |  | || | | | ||  | |  || | |   |  ||     | |  | |        | ||||| |   ||  | |||||| || ||||    |     || |   |    |  || | ||| |||| ||||||||||||||||||||| |||||||  | ||| ||||| | || |||||||| || |||
---------------------------------------gtaagtatgcttgtcttgaactatttattaatct-cacatgt-tgtttaattgt-catttgtcacacgatccatgtgaccattttaagcaaaaccttgttc--aatgaaaattctctgcttctaaacgattgataatttactttgcatttttcctgtagATTTTCTACTTTGTTGGATTTGGATTGTTCTGCATTGAAACATTGATCAGTATCTGGGTTATTCAG

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 12
gtaagctgatcacctttttgtttgctaaatcagatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctttgaaaattttgataaataatcatctagtatccttgatgcgaaacataattctatggttcttttggtaacctagtaatccacacgcttgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG
                |  || ||        ||  ||  ||  |||    | ||   | |  ||    || | |  | |   ||  ||      || |     ||||  |||   ||| |  ||    |     | |  |||   ||||||   |  || ||||  |   ||  |  | |   |  ||   ||| |||| ||||||||||||||||||||| |||||||  | ||| ||||| | ||  ||||||| || |||
---------------gtaagtatgactgtcttgaactacttac-tattaccacatgc-tgttaattgccatttgt-cacacg-atccatgcgacaattttaagcaaaaccttgtccaatgaaaattccctgcttctaa-acgattgataatttacttcttttttt--ttttcttttctttctttccatttacctgtagATTTTCTACTTTGTTGGATTTGGATTGTTCTGCATTGAAACATTGATCAGTGTCTGGGTTATTCAG

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 11
gtaagctgatcacctttttgtttgctaaatcagatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctttgaaaattttgataaataatcatctagtatccttgatgcgaaacataattctatggttcttttggtaacctagtaatccacacgcttgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG
                                                                                         | |  ||  |   |  |  ||     | |||  |||   |    || ||        |||   ||      |||||  |    |  |      |   ||| |  |  |||| ||||||||  |||| |||||| |||||||| | |||||| |||| ||||||||||| || |||
-----------------------------------------------------------------------------------------aaacctaggtgacttgaccttgcatgagatacacatgagggtctctaga--------atatcgctggaagccttttactggattgattgatttctt-cttttattatagATCTTCTACTTCATTGGGTTTGGAATGTTCTGTGTTGAATCAGTGCTCAGCATCTGGGTTATTCAG

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
gtaagctgatcacctttttgtttgctaaatcagatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctttgaaaattttgataaataatcatc-tagtatccttgatgcgaaacataattctatggttcttttggtaacctagtaatccacacg-cttgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG
                                                                                                   |||   ||||| | || |  | ||||  ||||  | ||  |        |  |||| |  |       | |      | ||  ||||  | | |  |||||||||||||| || ||||||||||| ||||||| || |||||| |||| || ||||||||  | |||
--------------------------------------------------------------------------------------------------ccttgacaaattattatcaggattcatggtagtggcttt--ttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG

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|60342784|gb|DN209757.1|DN209757
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|18384947|gb|BM418146.1|BM418146
EST:     GATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTCAGC
genomic: GATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|149103005|gb|EE288366.2|EE288366
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTTTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGNTGGATTTGGACTGTTCTGT
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGT
EST: gi|18384946|gb|BM418145.1|BM418145
EST:     GATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTCAGC
genomic: GATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|76018526|gb|DT945696.1|DT945696
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|29543932|gb|CB604312.1|CB604312
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|78023022|gb|DV491409.1|DV491409
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTCAGC
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTG-AATCATTGCTTAGC
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|110944605|gb|EE164762.1|EE164762
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTTTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGC
EST: gi|166654883|gb|EG281590.1|EG281590
EST:     AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG                         ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCT
genomic: AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCT

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: 195

AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 475

AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGgtaagctgat ... tgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacataattctatggttcttttggtaacctagtaatccacacgcttgttctgcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG
                     tggtaac  putative branch site (score: 475)
                                           cttgttct  putative PPT
     aattctat  TA-rich tract