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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcatgctaggatcagtcttatccttttggacagagccttaatttgtctctagtttatatacgctattactaaagctgattcacttggttacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA

Basic information

species Zea mays
transcript GRMZM2G031802_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031802_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 3
tatcatgctaggatcagtcttatccttttggacagagcct--taatttg---tctctagttt---atata-cgctattactaaagctgattcacttggttacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA
    ||| || | |   ||||  | |||||  |||   ||  || ||||   | ||||||||   |||||  |||||  || || |  |||   ||||| | |||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| || || |||||||
---gatgttatgttggatctt--cattttgttcagtttcttgtattttgccatttctagtttctgatataatgctatctctcaa-cacatt---ttggtgatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA

upper sequence: GRMZM2G031802_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G46570.2 (Glycine max), 3'ss of exon 3
tatcatgctaggatcagtcttatccttttggacagagccttaatttg---tctctagtttatatacgctattactaaagctgattcacttggttacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA--------------------------
 ||  |  || | |  ||   |  | |||| |       ||  ||||   ||  |   | ||| |    ||   || |      |    ||| | | ||||||||| ||| | |  || || || || |||||||| || || ||||| ||||||||||| |||||||| |||||||                          
-attcttataagctt-gttcaactcatttgaagtttttgtttgtttgaagtccgtgaatcataaaattcatgtttataatactattgtctggct-caatgcagTGCATACAGAGGACTATACATTCTCAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAGTATGATTCTCTCTTATTGTGTTTTA

upper sequence: GRMZM2G031802_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G46570.1 (Glycine max), 3'ss of exon 3
tatcatgctaggatcagtcttatccttttggacagagccttaatttg---tctctagtttatatacgctattactaaagctgattcacttggttacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA
 ||  |  || | |  ||   |  | |||| |       ||  ||||   ||  |   | ||| |    ||   || |      |    ||| | | ||||||||| ||| | |  || || || || |||||||| || || ||||| ||||||||||| |||||||| |||||||
-attcttataagctt-gttcaactcatttgaagtttttgtttgtttgaagtccgtgaatcataaaattcatgtttataatactattgtctggct-caatgcagTGCATACAGAGGACTATACATTCTCAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA

upper sequence: GRMZM2G031802_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------tatcatgctaggatcagtc-----ttatccttttggacagagccttaatttg-----tctctagtttatatacgct-attactaaagctgattcacttggttacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA
                                                     | || ||   ||||   ||      | | || |||   |   |  ||||||       ||||   ||  ||||    ||| ||| | |       ||   ||    ||||| |  |||||||   | || ||||| |||||||| ||||| |||||||||||||| || ||||| ||||||||||
gtacgatcttctttccataacttccctttacttgaaatttatcgttgcgtcgttctcttgactggatacatcattgactgttctcttgccaaactctataatttagtttccctctgagtttcatacttcgattgctataccaataatgctctcttct--tgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA

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|166487095|gb|EG283683.1|EG283683
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACT
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACT
EST: gi|148995872|gb|EE035110.2|EE035110
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|71425662|gb|DR806812.1|DR806812
EST:     GGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: GGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|211132529|gb|FL458973.1|FL458973
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|60397063|gb|DN229882.1|DN229882
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|5361053|gb|AI795668.1|AI795668
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|60359236|gb|DN226209.1|DN226209
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|71425663|gb|DR806813.1|DR806813
EST:     GGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: GGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|71329461|gb|DR801451.1|DR801451
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|78117678|gb|DV536065.1|DV536065
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|8383313|gb|BE056256.1|BE056256
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|5847439|gb|AW000518.1|AW000518
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|67022873|gb|CO451622.1|CO451622
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
EST: gi|78117677|gb|DV536064.1|DV536064
EST:     CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTTTGGG                         TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA
genomic: CGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGA

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), 48 (downstream exon)
Score: 84

CCATTTATTTGGAAGCTGTCGCGATATTTCCACAACTTGTGTTGCTACAGCGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 92

CCATTTATTTGGAAGCTGTCGCGATATTTCCACAACTTGTGTTGCTACAGCGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

CCATTTATTTGGAAGCTGTCGCGATATTTCCACAACTTGTGTTGCTACAGCGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

CCATTTATTTGGAAGCTGTCGCGATATTTCCACAACTTGTGTTGCTACAGCGGACAAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTCTTGGGgtaagagatc ... tacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctctagtttatatacgctattactaaagctgattcacttggttacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA
      tagtttatata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcatgctaggatcagtcttatccttttggacagagccttaatttgtctctagtttatatacgctattactaaagctgattcacttggttacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA

- -catgcta
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