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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactgggaatattgtttaactttcttggtctcttctaacaggattctttctgctgaaaggataccagtaacttagacatgctcactagtcttgttgttttag

Basic information

species Zea mays
transcript GRMZM2G143862_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 10
AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactgggaatattgt-ttaactttcttggtctcttctaacaggattctttctgctgaaaggataccagtaacttagacatgctcactagtcttgttgttttag
||||||||||||  | ||||| ||| | |||||||| ||  |||||||||| || |||||||||||| |||||||||||||||| ||||| |||||||||||||| | |   | |  |   ||  ||  | ||   | ||     ||  ||  |  | || |        |  |||||      || |    | | |||||  |||||
AAGCAAGCTTCAACCAGAATCCAGGCAACTGTTTGACTTCCTGCCCAAAACCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaag------tccctaactgg----tgttggaaatttttgtt--tttag

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 10
AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactggga-atattgtttaactttcttggtctcttctaacag-gattctttctgctgaaaggataccagtaacttagacatgctcactagtcttgttgttttag
 |  || ||    | | | |||    |||| ||||| ||||| || ||| | ||||| || ||| | ||||||||||||||||| ||||| |||||||||||    | ||    ||| |  |  |||| ||  || | |  |  | |  || |  | ||   ||     |    |    || | ||   || |                
GAAGAAACTCACCGATCAGTCATTAAAGCTTTTTGAATTTTTACCTAAAGCAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatgtattatagttctatacttgctgtgtttatcttgcctgtaatgcaatttgactaagcctcaatgttgg--tatatatttccatttag-------------

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 10
AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactgggaatattgtttaactttcttggtctcttctaacaggattctttctgctgaaaggataccagtaacttagacatgctcactagtcttgttgttttag
 |  || ||    | | ||||   | |||| ||||| ||||| ||  || | ||||| |||||| | ||||||||||||||||| ||||| |||||||||||    | ||    ||| ||   |  ||  ||   |  | |  |     | |      ||||  |  |||| |   |||  | ||||     || |||   |||   
GAAGAAACTCACTGATCAATCGTTGAAGCTTTTTGACTTTTTACCTCAAGCAATTCAAGAGCAATTGATGCTTGAAAGAGATCCACATGGAAATGTTCAGgtgcctaatgttgttatagtgctatcttgctgtgtttatttggctcctctatccaatttgaagcggcaccaatg--ttaatcttgctt----gtattgccatttag-

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 10
AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactgggaatattgtttaactttcttggtctcttctaacaggattctttctgctgaaaggataccagtaacttagacatgctcactagtcttgttgttttag
 |  || ||    | | |||||  | |||| ||||| ||||| ||  || | ||||| || ||| | ||||||||||||||||| ||||| |||||||||||    | ||    ||||||   |  ||  |||  |  | |  |         |||    ||   | | | | | ||  |  |  ||  |  || ||    |||   
GAAGAAACTCACTGATCAATCATTGAAGCTTTTTGACTTTTTACCTCAAGCAATTCAAGAACAATTGATGCTTGAAAGAGATCCACATGGAAATGTTCAGgtgcctaatgttgttattgtgctatcttgctgggttgatttggc------tcctctatccaatttaaatcggcacctatgttaatcttgcctgtattcccatttag-

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G01360.1 (Glycine max), 5'ss of exon 8
AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactggga-atattgtttaactttcttggtctcttctaacaggattct-ttctgctgaaaggataccagtaacttagacatgctcactagtcttgttgttttag
 |  || ||    | | | |||    |||| || || ||||| || ||| | || || || ||| | ||||||||||||||||| ||||| |||||||||||    | ||    ||| || |  ||||| |   |  | | |||    |||    |  ||   || | |   |   | ||  |  |                       
GAAGAAACTCACTGATCAGTCATTAAAGCTTTTCGAATTTTTACCTAAAGCAATGCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatgtattatagtgctatactttatct-tgccctgtaatgcaatttgactaagcctcaatgttggtatatatttccatttag---------------------

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 10
AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactgggaatattgtttaactttcttggtctcttctaacaggattctttctgctgaaaggataccagtaacttagacatgctcactagtcttgttgttttag
||  || |||     | | ||   | | |||||||| ||| | ||   | | |||||||| ||| | ||||||||||||||||| ||||| ||||| |||||    |      ||  |  |  |  |   |  |      | ||  | ||  |  | |||| ||       || | | | |       |   || ||  |   ||||
AAAGAAACTTACAAATCAGTCTCTGCAACTGTTTGAATTTCTACCTCCAGCAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatcttatatgctagtatatgtgtgtatttgaactttacttg-tttgtaattctgatagatctttggttattgata-------atctgtttttataccttag

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|22521075|gb|BU079886.1|BU079886
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|211507305|gb|FK969872.1|FK969872
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|32932722|gb|CF037534.1|CF037534
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|213170617|gb|FM193174.1|FM193174
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAA                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|148934427|gb|EC878461.2|EC878461
EST:     CTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|67023546|gb|CO452295.1|CO452295
EST:     TGGCAATGTTCAG                         GTTGC-AAAATTG-AACTGAGAAAA-GCTTATTAGCATGGTGGAAACTGAA
genomic: TGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|37398696|gb|CF636665.1|CF636665
EST:     GGCAATGTTCAG                         GTCGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: GGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|211507302|gb|FK969869.1|FK969869
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|67015451|gb|CO444200.1|CO444200
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|67024935|gb|CO453684.1|CO453684
EST:     GAGATCCCCTTGCGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: GAGATCCCCATG-GCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|211182047|gb|FL030523.1|FL030523
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|60343399|gb|DN210372.1|DN210372
EST:     CCCCATGGCAATGTTCAG                         GTTGCAAAAA-TGAAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGA
genomic: CCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTG-AAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGA
EST: gi|67012343|gb|CO441092.1|CO441092
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|211507300|gb|FK969867.1|FK969867
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|87155550|gb|DY400339.1|DY400339
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|32930610|gb|CF035422.1|CF035422
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|166703126|gb|EG174627.1|EG174627
EST:     CAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAA-TTGAAACTGAGAAA-TGCTTATTAGCATGGTGGAAACTGAA
genomic: CAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|26558921|gb|CA831156.1|CA831156
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
EST: gi|211507306|gb|FK969873.1|FK969873
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAA

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: 340

AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAAGCTGAGGGGAGATACTCTGCACATTTCAGAGGAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 313

AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAAGCTGAGGGGAGATACTCTGCACATTTCAGAGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 425

AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAAGCTGAGGGGAGATACTCTGCACATTTCAGAGGAC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 369

AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactg ... gttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAAGCTGAGGGGAGATACTCTGCACATTTCAGAGGAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCAAGCTTCAGGCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAAAACTATTCAGGAGCAACTTATGCTTGAAAGAGATCCCCATGGCAATGTTCAGgtaaagactgggaatattgtttaactttcttggtctcttctaacaggattctttctgctgaaaggataccagtaacttagacatgctcactagtcttgttgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC