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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttccttgaaatgcatagaaaatcatgttaactgcataaacaaaaatgtcatacaaagaaagttatttcagctcttgaatattgttactcatgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA

Basic information

species Zea mays
transcript GRMZM2G020446_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 5
gtttccttgaaatgcatagaaaatcatgttaactgcataaacaaaaatgtcatacaaagaaa----gttatttcagctcttgaatattgttactcatgtg--gcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA---
     |   |||||   | || |  |  | || |  | |  ||   || || ||| | |        | || | |  |       ||   ||  ||  ||  |||||||||||||||||| |||||  ||   || | ||| |||| ||| || |||||||||||||||||||||||||| ||||||||||||||||| ||||| |   
-----caacaaatgttcaaaataa-acatgaaatatacattcagttatttcgtactatgttgttttatcatgttatttacctgtcatctctatccacatggtgcagCATATCGAACTGGTTTCTCCTTCC---CCAGATGCAGAAGTAGCAACATTCGATATTGTTGGACCAGTTTGTGAATCTGCAGATTTCCTTGGCAAAGACAGGG

upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G06090.1 (Glycine max), 3'ss of exon 9
---------gtttccttgaaatgcatagaaaatcatgttaactgcataaacaaaaatgtcatacaaagaaagttatttcagctcttgaatattgttactcatgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA
          | |   | ||||||  |     |  || |   |  |||  || |||| || |       ||  ||||  |    |   || | |||  |   || |||||||||||||||||| || ||  || |  | | ||||||   ||| |  || ||| || |||| || || |||||||||||||||||| ||||||||||||
ccatttctgatgttactcaaatgc-catttggttgtgcttttt-tatattcagaaatttcttttccttgaa--tattgaa----tgacatgtcgttgttt-cgttgcagCATATCGAACTGGTTTCCCCTGCCCCAGCAGATGCTGAGATAGCAAAGTTTGATGTTCTTGGTCCTGTCTGTGAGTCTGCAGATTTCTTTGGAAAAGATA
















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|16379536|gb|BI993011.1|BI993011
EST:     ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAG                         CATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
genomic: ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
EST: gi|76928256|gb|DV171541.1|DV171541
EST:     ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAG                         CATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCGGAAGCAGCGACCTTC
genomic: ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
EST: gi|211042194|gb|FL157904.1|FL157904
EST:     ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCCCCCACTCCTGGTGCTGAAGTAGCGACCTTC
genomic: ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
EST: gi|13515636|gb|BG517912.1|BG517912
EST:     AGTCTGTATGGAGCATACCAG                         CATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
genomic: AGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
EST: gi|78123739|gb|DV542123.1|DV542123
EST:     ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAG                         CATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
genomic: ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
EST: gi|211042195|gb|FL157905.1|FL157905
EST:     ATGGCAGCATGGCAGAACTCATCAGACCTAGCCTGTATGGAGCATATCAG                         CATATCGAATTGGTCTCTCCCCCCACTCCTGGTGCTGAAGTAGCGACCTTC
genomic: ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
EST: gi|211076903|gb|FL402120.1|FL402120
EST:     ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAG                         CATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGTAGCGACCTTC
genomic: ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
EST: gi|148934358|gb|EC878387.2|EC878387
EST:     ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAG                         CATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC
genomic: ATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTC

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: 284

TAGAGTAACTGGTGTTAAATCTAATGGTACAAAGAATTTCATTGTTGTTGATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 189

TAGAGTAACTGGTGTTAAATCTAATGGTACAAAGAATTTCATTGTTGTTGATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

TAGAGTAACTGGTGTTAAATCTAATGGTACAAAGAATTTCATTGTTGTTGATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 150

TAGAGTAACTGGTGTTAAATCTAATGGTACAAAGAATTTCATTGTTGTTGATGGCAGCATGGCAGAACTCATCAGACCTAGTCTGTATGGAGCATACCAGgtttgtttta ... catgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtcatacaaagaaagttatttcagctcttgaatattgttactcatgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA
          aaagaaagttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttccttgaaatgcatagaaaatcatgttaactgcataaacaaaaatgtcatacaaagaaagttatttcagctcttgaatattgttactcatgtggcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - -atgcata
- - - - - - - - - - - - catgtta
- - - - - - - - - - - - - - - - ctgcata
- - - - - - - - - - - - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttact