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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttttccccctcacattctggggaagccatgtaggcgtgtttgttttcagcaccagattgtctggccaggcagcaacctaagccgtcgttcataccatgattctaacatgtggaacattatggtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTGATATCTGCAGTGTTGCTGTTTTTCGTTGCCTTCATTGCGTATCTTCACA

Basic information

species Zea mays
transcript GRMZM2G177273_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177273_T01 (Zea mays), 3'ss of exon 7
lower sequence: 13113.m00157 (Oryza sativa), 3'ss of exon 8
gtacttttttccccctcacattctggggaagccatgtaggcgtgtttgttttcagcaccagattgtctggccaggcagcaacctaagccgtcgttcataccatgattctaacatgtggaacattatggtgc--ctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTGATATCTGCAGTGTTGCTGTTTTTCGTTGCCTTCATTGCGTATCTTCACA
        | | | || |||     |  | ||| || |  | | ||||  ||         ||||||||          ||  |  || || ||  | ||  |   ||| | | |    ||||   ||  |  ||  ||||||| || ||||||||||||||||||||||| || ||||| |||||||||||||| || ||||| ||||| || || |||| |||||| ||||||||||
-------gtactctctgaca-----gataggccttg-atacatttttgaatttgattggtaattgtctg----------aatgtt-gctgttgtg-agactcta--tctgataagcatgacatctcggctcaactgcagGTGTATTACGAATTCAATCCGATCTTCATGCTCGCAGAACCGTTGATGCTGATATCAGCCGTGTTCCTGTTCTTTGTAGCCTGCATTGCTTATCTTCACA
















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|78024949|gb|DV493336.1|DV493336
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|6654207|gb|AW267612.1|AW267612
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|5455857|gb|AI833547.1|AI833547
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCCCAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|166703330|gb|EG124319.1|EG124319
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAA
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAA
EST: gi|211408847|gb|FL082357.1|FL082357
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|37387875|gb|CF631140.1|CF631140
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|78023626|gb|DV492013.1|DV492013
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|22542436|gb|BU092874.1|BU092874
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|5468696|gb|AI834487.1|AI834487
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|17921687|gb|BM259338.1|BM259338
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|78075801|gb|DV504235.1|DV504235
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|20803243|gb|BQ294293.1|BQ294293
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|21331859|gb|BQ487240.1|BQ487240
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCCTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|71763848|gb|DR961785.1|DR961785
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|23199481|gb|BU582046.1|BU582046
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCCTTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|5069740|gb|AI737705.1|AI737705
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|74236700|gb|DT644614.1|DT644614
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|60397407|gb|DN230223.1|DN230223
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
EST: gi|60352174|gb|DN219147.1|DN219147
EST:     TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG                         GTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG
genomic: TTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTG

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: 45 (upstream exon), 49 (downstream exon)
Score: 215

ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTGATATCTGCAGTGTTGCTGTTTTTCGTTGCCTTCATTGCGTATCTTCACA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 139

ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTGATATCTGCAGTGTTGCTGTTTTTCGTTGCCTTCATTGCGTATCTTCACA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 103

ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTGATATCTGCAGTGTTGCTGTTTTTCGTTGCCTTCATTGCGTATCTTCACA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 239

ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAGgtactttttt ... gtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTGATATCTGCAGTGTTGCTGTTTTTCGTTGCCTTCATTGCGTATCTTCACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaagccgtcgttcataccatgattctaacatgtggaacattatggtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTGATATCTGCAGTGTTGCTGTTTTTCGTTGCCTTCATTGCGTATCTTCACA
                       ttctaac  putative branch site (score: 239)
                                              tgccttt  putative PPT
                                    aacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttttttccccctcacattctggggaagccatgtaggcgtgtttgttttcagcaccagattgtctggccaggcagcaacctaagccgtcgttcataccatgattctaacatgtggaacattatggtgcctttagGTGTACTATGAATTCAATCCGATCTTCATGCTGGCGGAACCATTGATGCTGATATCTGCAGTGTTGCTGTTTTTCGTTGCCTTCATTGCGTATCTTCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT