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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggccttctcatgctgaaatagttttcatttcattaatgactagatttacttaaacagttttatcaaacagatcactatgcttgacacagttatgatatttctatcggtattctctttctag

Basic information

species Zea mays
transcript GRMZM2G117507_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 10
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggccttc-----tcatgctgaaatagttttcatttcattaatgactagatttacttaaacagttttatcaaacagatcactatgcttgacacagttatgatatttctatcggtattctctttctag
| ||||||||||| ||||||||||||||  | |  ||||| || || ||||| || || ||||||||||| ||||| |||||||||||||  ||||||||||||||||||      |||     ||||| |  |||  | || ||| | || |||| |||   || |  | | ||  |  |   | |  |   |    || | | |||| ||| ||||||||| |  |||
GAGCAATTGCTATAATGAGCCACCCAATTGCAAGCACAAATGACTCTCACTCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctttctcaatcacaaacaaatactgctcaccttatgaattattacatttgcttgcccattgcttttaacaaagtttatttattc--ccattttgtaacatttttattggtattctcctgttag

upper sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 10
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt-ctcatgctgaaatagttttcatttcattaatgactagatttacttaaacagttttatcaaacagatcactatgcttgacacagttatgatatttctatcggtattctctttctag
| || |||||||| ||||||||||| ||  | || ||||| || || ||||| || || ||||||||||| ||||| |||||||||||||  |||||||||||||||||| | ||  || ||  | || ||||   || ||| ||||||||| |||   || |  | | ||  ||     ||| ||   | || ||| |  |||||||| ||||||||| |  |||
GCGCTATTGCTATTATGAGCCACCCGATTGCAAACACAAATGACTCGCACTCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctttcgcaatctcaatcacttctcatcagatgaattactagatttgcttgcccattgcttttaataag----ttattctatccccatttacggaatttctattggtattctcctgttag

upper sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 10
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggccttctcatgctgaaatagttttcatttcattaatgactagatttacttaaaca-gttttatcaaacagatcactatgcttgacacagttatgatatttctatcggtattctctttctag
| || ||     |||||||||| ||||| || ||||| |  || ||  | ||||||||||| ||| |||| || ||||||||||| |||||||||||||||| ||      || ||      ||| |||      || ||||| || | |||   ||    || | |||       |  ||| | ||| | ||   | |  || | |  |   |            
GCGCTATCTGCTTCATGAGCCATCCAATTCCAAATACTAGTGACTCTGATTCGGTTCAAATAATTCTGCCGCAAAAGCAACTTGGTCGCAGATCAGACATgtaag------tcgtg------tagcttt------ataaatgattaaaattatgaaatggtgtataatcgtttgtgttgctaagtttggctcaaagaggg-atcttttacaacacatca-------

upper sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 10
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggccttctcatgctgaaatagttttcatttcattaatgactagatttacttaaacagttttatcaaacagatcactatgcttgacacagttatgatatttctatcggtattctctttctag
|||| ||     |||||||||||||||| || ||||| ||  | ||  |||| |||||||| ||| |||| |||||||||||||| |||||||||||||||| || || | |  |  ||   |  |||| |        |    |  | ||| ||       | ||  |     |||     | |||||    |||| || | |                     
GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaag-ccgtgtacttttggtttgattttaaacaggaggagatgtccaattatttgggttcctgtaaaatttgaatcga---ggttgacctgtttataatctat---------------------

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|60351459|gb|DN218432.1|DN218432
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|32930550|gb|CF035362.1|CF035362
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|6827485|gb|AW331128.1|AW331128
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|5296179|gb|AI782859.1|AI782859
EST:     TCNNNNNNNATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|211070323|gb|FL464130.1|FL464130
EST:     CAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: CAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|32932215|gb|CF037027.1|CF037027
EST:     TCGGTTCAAATTATTTTGCCTCATAAGCAACTTGTACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|31352817|gb|CD437174.1|CD437174
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|60346246|gb|DN213219.1|DN213219
EST:     TCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|29946000|gb|CB815928.1|CB815928
EST:     CAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCNCCAGGAGGGAAGTT
genomic: CAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|60353508|gb|DN220481.1|DN220481
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|6056470|gb|AW090860.1|AW090860
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|6194638|gb|AW146742.1|AW146742
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|5901301|gb|AW042401.1|AW042401
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|32934162|gb|CF038974.1|CF038974
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|32934507|gb|CF039319.1|CF039319
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTT
EST: gi|15313508|gb|BI478735.1|BI478735
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAG
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAG
EST: gi|5895558|gb|AW036804.1|AW036804
EST:     TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACAT                         GTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAG
genomic: TCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAG

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: 667

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAATCCCCAGTCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 918

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAATCCCCAGTCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 659

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAATCCCCAGTCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 415

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggcctt ... ctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAATCCCCAGTCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggccttctcatgctgaaatagttttcatttcattaatgactagatttacttaaacagttttatcaaacagatcactatgcttgacacagttatgatatttctatcggtattctctttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA