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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggccttctctcatgttgaactagtttcatctcatgttgaacacttttatcgaacagatcactatgcttgacacaattatgatatttctgtcggtattctctttttag

Basic information

species Zea mays
transcript GRMZM2G435373_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 10
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggccttctctcatgttgaactagt-ttcatctcatgttgaacacttttatcgaacagatcactatgcttgacacaatt----------------atgatatttctgtcggtattctctttttag
| ||||||||||| ||||||||||||||  | |  |||||||| || ||||| || || ||||||||||| ||||||||||||||||| |  |||||||||| |||||||     ||    ||| | |  |  || | |  ||||   ||  ||      |  || |    || ||| | ||                 | | |||| | | ||||||||| | ||||
GAGCAATTGCTATAATGAGCCACCCAATTGCAAGCACAAATGACTCTCACTCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctttctcaatcacaaacaaatactgctcaccttatgaattattacatttgcttgcccattgcttttaacaaagtttatttattcccattttgtaacatttttattggtattctcctgttag

upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 10
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggccttctctcatgttgaactagtttcatctcatg-----ttgaacacttttatcgaacagatc------actatgcttgacacaattatgatatttctgtcggtattctctttttag
| || |||||||| ||||||||||| ||  | || |||||||| || ||||| || || ||||||||||| ||||||||||||||||| |  |||||||||| |||||||     || |  | |   | |||||  |||      |  |     ||  | |     |         ||| ||   | || ||| |  |||||| | ||||||||| | ||||
GCGCTATTGCTATTATGAGCCACCCGATTGCAAACACAAATGACTCGCACTCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctttcgcaatctcaatcacttctcatcagatgaattactagatttgcttgcccattgcttttaataagttattctatccccatttacggaatttctattggtattctcctgttag

upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 10
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggccttc--tctcatgttgaactagtttcatctcatgttgaacacttttatcgaacagatcactatgcttgacacaattatgatatttctgtcggtattctctttttag
| || ||     |||||||||| ||||| || ||||| | ||| ||  | ||||||||||| ||| |||| || || |||||||| || |||||||||||||||| | |      | ||     | ||   | ||   ||| || | |     ||||      |  ||| | ||| | |||  | |  || | |  |   |            
GCGCTATCTGCTTCATGAGCCATCCAATTCCAAATACTAGTGACTCTGATTCGGTTCAAATAATTCTGCCGCAAAAGCAACTTGGTCGCAGATCAGACATgtaagtcgtgtagctttataaatgattaaaattatgaaatggtgtata-----atcgtttgtgttgctaagtttggctcaaaga-gggatcttttacaacacatca-------

upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 10
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggccttctctcatgttgaactagtttcatctcatgttgaacacttttatcgaacagatcactatgcttgacacaattatgatatttctgtcggtattctctttttag
|||| ||     |||||||||||||||| || ||||| ||| | ||  |||| |||||||| ||| |||| ||||| |||||||| || |||||||||||||||| | |   ||    |||   |  ||| |   || |  ||    |   ||      | |  || |         |||   | |    ||||   || ||| |      
GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtgtactt---ttggtttgattttaaa-caggaggagatgtccaattatttgggttcctgtaaa-atttgaatcgaggttgacctgtttataatctat------

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|24934285|gb|CA452503.1|CA452503
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|67031426|gb|CO460175.1|CO460175
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|60396805|gb|DN229633.1|DN229633
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|33095264|gb|CF055258.1|CF055258
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTACATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|32856054|gb|CD995735.1|CD995735
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|47962286|gb|CN844995.1|CN844995
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|33102234|gb|CF062194.1|CF062194
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|211034436|gb|FL381555.1|FL381555
EST:     TCGGGTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAG                         GTATGTTTTCGGGTGTTCATACACGC
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGC
EST: gi|211445979|gb|FL406296.1|FL406296
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATATTGCGCCA
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCA
EST: gi|33095120|gb|CF055114.1|CF055114
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|211259815|gb|FL426651.1|FL426651
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATG
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATG
EST: gi|67021306|gb|CO450055.1|CO450055
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTATATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|32933839|gb|CF038651.1|CF038651
EST:     AGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: AGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|60359326|gb|DN226299.1|DN226299
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|30087662|gb|CB885868.1|CB885868
EST:     GGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: GGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|32919393|gb|CF024205.1|CF024205
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|113704014|gb|EE681518.1|EE681518
EST:     ATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: ATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|211346475|gb|FL413228.1|FL413228
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|5915143|gb|AW052784.1|AW052784
EST:     ATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: ATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|33093030|gb|CF053024.1|CF053024
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|60355746|gb|DN222719.1|DN222719
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|32930298|gb|CF035110.1|CF035110
EST:     AGATCAGACAT                         GCATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: AGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|149098466|gb|EE184445.2|EE184445
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|67014412|gb|CO443161.1|CO443161
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
EST: gi|211493511|gb|FL163239.1|FL163239
EST:     TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTATATCAGACAT                         GTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT
genomic: TCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTT

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: 160

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAACCCGCAATCTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 142

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAACCCGCAATCTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAACCCGCAATCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggcctt ... ctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAACCCGCAATCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggccttctctcatgttgaactagtttcatctcatgttgaacacttttatcgaacagatcactatgcttgacacaattatgatatttctgtcggtattctctttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA