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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 11
gtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG
||   |  ||||||| | ||   | |  ||  ||       |  |||||     |  |  | ||     | ||  || | |   ||| |   ||   |||  |||         | || || |  | ||  || |   ||| | ||||||||||||||| | |||||||| |||||||| |||||||| || ||||| || |||||||| ||||||||||| |||||||| || |||||||||||||
gtacttctttctttctttaccaatctcatatttg-------tgattctttaaggtggtgttgttcgctatttgtcatgtaacacattgt--ttacatattgctctg-------tctaattattcctactctca-taatcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG

upper sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 10
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------------gtgtgttattctttcataacttgtttt----ctacgtgctggaa--ctagttcttctgatttcttatctttctagtatgctatctta--tggattctagctattcatttt---tctagaaaggacccaa---ctaatgattcttg-caattgcct-----ttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG
                         |   ||| ||| || |  ||||||    || | |  || ||  | | |||| |  | |||  | |        |     | ||   ||      |   ||   ||||   | |   | || |   |   | | ||| ||    |||  || |      | ||||||||| |||||| | || ||||| |||||||||||| |||| |||||||||||  | || |||||||| || |  ||  || |  | || ||||||||  
gtaaacatctacaacttcttttcaattaaatttttttattagatgtttttgtactccattttgaaataccacttctgcccaattcacaaccccaccacacaaggttttgagtgagcaacacacatgggttttgagtttttgaggggcatgaagtccattgaatcccatcaacagcatattcactttcagATGGCAGAGTATAGAATTTCTATCTATGGGAGGAAGGAAAGTGAATGGGACCAGTTAGCCAGTTGGATTGTCACTAACAAACTTCAAAGTGAGAATGTGA

upper sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 10
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 10
gtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG
                                   || ||      || |||      ||| || ||||||  || | |  |  |  |||   | || ||   || | || ||  ||  | | |||  |||    | | ||    |||||||||||||| ||||||| ||||| || |||||||| || || ||||| ||| ||||   |||||| ||  ||||| |  |  | || ||||| ||  
-----------------------------------tgaaaa----cctcctg----tctatgttgctagtactctttatctttaaaactaa--aatccttccacttgcaaagaatca--tgacgatatttgtctgttcgttgtgtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA

upper sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 10
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 10
gtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatc--agATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG
                                | |  |||     |  |    ||   |  ||||  ||  |          | | |    |  |  ||   | || |||      ||| ||| |    |  | ||| || |     |||||||||||||  ||||||| ||||| || |||||||| ||||| ||||| ||  ||||||||||||||||  |||||    | || || || || ||  
-------------------------------atacgcgaatggcgttgttaacttggatgacttttaagcgta---------gaact---acggtgtatccgtttacaaa------aacaaataacctgtttatttgtctgtgatgtagATGGCTGAGTACAGGATATCAATTTACGGAAGGAAGAAGAGCGAGTGGGATCAGTTGGCAAGTTGGATAGTTGACAATCGGCTGTACAGTGAAAACGTCA

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|71772853|gb|DR970776.1|DR970776
EST:     CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATC
genomic: CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATC
EST: gi|74237693|gb|DT645607.1|DT645607
EST:     GAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
genomic: GAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
EST: gi|71299098|gb|DR785546.1|DR785546
EST:     CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
genomic: CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
EST: gi|32835884|gb|CD975562.1|CD975562
EST:     CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
genomic: CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
EST: gi|32863100|gb|CF002782.1|CF002782
EST:     CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
genomic: CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC

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: 238

GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 303

GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 137

GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG
                        aactaat  putative branch site (score: 137)
                                          ttgccttt  putative PPT
     atttttcta  TA-rich tract