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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgttgatgcaactattcttcatgacttgatgtacctaccaaaatcatgactcatagtcttgggctctcattgtttttggtgaaatttgaagtgtcaaagtggcggacttctaatttcattcattctacttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC

Basic information

species Zea mays
transcript GRMZM5G836910_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 6
gtaagtatgttgatgcaactattcttcatgacttgatgtacctaccaaaatcatgactcatagtctt-gggctctcattgtttttggtgaaatttgaagtgtcaaagtggcggacttctaatttcattcattctacttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC
                                     |||  ||    ||| |     | || |||| | ||  |||   |  ||  | | |   || |||||  | ||||  ||||  || | || ||  | | |||    ||||| || |||||||| || ||||||||||| | ||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||
-------------------------------------gtatgtatgtgaattaatgtgcttaatctttgagcattcaacttcatttttcatagcaga-gtgtctcattggcaaactttgaactccaatctatattctt----acagGCAATCACAAGAACATTTTCAATGATGCAAAGGTACCTTGGTCAGAGTACCGTTATTACGACCCCAAGACTGTTGGCTTGGATTTTGAGGGAATGATAGC

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 6
gtaagtatgttgatgcaactattcttcatgacttgatgtacctaccaaaatcatgactcatagtcttgggctctcattgtttttggtgaaatttgaagtgtcaaagtggcggacttctaatttcattcattctacttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC
                                                    |||  |  || |  |   | || |||   || |  |  || |    |    |  |     |   ||  |  |||| ||| | |||||    |||||| ||||||||||| |||||||||||||| || || ||||| |||||||| |||||||| |||||||| |||||||||||||||||||| ||||| | 
--------------------------------------------------gtatgcattttactgctt--ccctgattaacttggtcgtgatatttgttagggagttcaaacatccctggtaacatt-attgt-cttgt----agGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGA

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G13480.2 (Glycine max), 3'ss of exon 6
gtaagtatgttgatgcaactattcttcatgacttgatgtacctaccaaaatcatgactcatagtcttgggctctcattgtttttggtgaaatttgaagtgtcaaa-gtggcggacttctaatttcat---tcattctacttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC
                                                              || |    ||  |    | | || | || || |  |||  |   ||   ||| ||| ||  || |   | |   || |   |  ||||||| ||||||||||| |||||||||||||| || || ||||| |||||||| |||||||| |||||||| ||||| |||||||||||||| ||||||| 
--------------------------------------------------------------gtatgtatctgactgcttctctgcttaacttggtcgtgatacttgtttgggagttcaaacatcctgggtaacattattgtcttgcagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGCTTGGATTTTGAGGGCATGATAGA

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 7
gtaagtatgttgatgcaactattcttcatgacttgatgtacctaccaaaatcatgactcatagtcttgggctctcattgtttttggtgaaatttgaagtgtcaaagtggcggacttctaatttcattcattctacttgttaa--cagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC
                                                          ||| ||||||  | |  |   ||||  ||||  ||||  || ||| | |      | | ||   |||    | | |  |   |   ||||||| ||||||||||||||||||||||| |  || || ||||| || ||||| || ||||| || || ||  |||| |||||||||||||||||||||||
-------------------------------------------------------gtacattgtcttgaccacaaacatttttgagtga--tttg--gtttcatatttaaccgccttta---tcaactgtacaaaataccacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtatgttgatgcaactattcttcatgacttgatgtacctaccaaaatcatgactcatagtcttgggctctcattgtttttggtgaaatttgaagtgtcaaagtggcggacttctaatttcattcattctacttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC
                                                                  || |   ||    | ||||| || |||||   ||||||     | || |||| ||    || |     | | ||  ||||||| ||||||||||| |||||||||||||| || || ||||| || ||||| || |||||||| || || ||||| ||||||||||| || |||||| |
-----------------------------------------------------------------gtgagtattccccttgtttgg-gagatttg---tgtcaagagtactgatttctcatg--gttgaagaatcatctttgcagGTAATCACAAGAATATTTTCAATGATGCTAGAGTTCCCTGGTCTGAATACCGATACTATGACCCAAAAACAGTTGGCTTGGATTTTGATGGGATGATATC

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|26557436|gb|CA829671.1|CA829671
EST:     ACAAAGATACTTTCCTGAAGCTAAAG-GCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|32863795|gb|CF003477.1|CF003477
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACA
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|32802835|gb|CD955071.1|CD955071
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATACTAGGGTACCTTGGTCAGAGTACA
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|5342983|gb|AI795288.1|AI795288
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACA
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|71440750|gb|DR821800.1|DR821800
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGTTCAGAGTACC
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|13515691|gb|BG517967.1|BG517967
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|149107658|gb|EE189537.2|EE189537
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|32788347|gb|CD940583.1|CD940583
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACA
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|148941508|gb|EC886438.2|EC886438
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|78114229|gb|DV532618.1|DV532618
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|149000841|gb|EE038069.2|EE038069
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|91056033|gb|EB166451.1|EB166451
EST:     CTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTA-GGTACCTTGGTCAGAGTACC
genomic: CTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC
EST: gi|211140317|gb|FL028762.1|FL028762
EST:     CAAAGATACTTTCCTGAAGCTAAGGTGCTGATATCGTCGCCCTACCTGGG                         GTAAC-ACAAGA
genomic: CAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCC-TACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGA
EST: gi|211139376|gb|FL028747.1|FL028747
EST:     ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGGCTACCTGGG                         GTAAC-ACAAGAA-ATCTTC
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTC
EST: gi|26557367|gb|CA829602.1|CA829602
EST:     ACAAAGATACTTTCCTGAAGCTAAAG-GCTGATATCGTCGCCTACCTGGG                         GTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAATACC
genomic: ACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACC

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: 105

CTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCAGCATTCATACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 526

CTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCAGCATTCATACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 69

CTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCAGCATTCATACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 406

CTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCAGCATTCATACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGCCTACCTGGGgtaagtatgt ... ttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgaagtgtcaaagtggcggacttctaatttcattcattctacttgttaacagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC
                        ttctaat  putative branch site (score: 406)
                                       ttctactt  putative PPT
                           taatttcattcatt  TA-rich tract