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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatacagattatttcttcaacacatttgaacaatttaagcagaagcataatcctttacacagtgtttttcgctaacttcaattggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG

Basic information

species Zea mays
transcript GRMZM2G420310_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 8
taatacagattatttcttcaacacatttgaacaatttaagcagaagcataatcctttacacag-tgtttttcgctaacttcaat--tggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG
  ||   ||  |   ||| ||    |||      ||| ||||    || | |  | | ||  | | |  ||  |||||||  ||   |   | | ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| || ||||||||||||||||
-tattttgaaaacagctttaagtttttttcttttttttagcattt-caca-ttttgtgcatggatttgcttttctaacttatatagcgcgcgatatttgtcagGCGAGGGTCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGCTATGTCAGTGGTGGCCTCTACTCAAGGAATGGTG

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 8
taatacagattatttcttcaacacatttgaacaatttaa-gcagaagcataatcctttacacagtgtttttcgctaacttcaattggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG
||  || || | || | |      | ||   | ||| |    |      |  ||   | |       ||     | |  | | ||   |    | || ||| ||||| || ||  |||||||||||||||| ||||||||||| |||||||| |||||||| ||||| ||||| ||  | |||||| | ||||| |
tatcactgaatgttccattcctctagttttcctattgactatattttttttgtcgacttcttctcccttcattattatgtaagtttccttcaatgtg-cagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGTAATGGGG

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 8
taatacagattatttcttca-acacatttgaacaatttaagcagaagcataatcctttacacagtgtttttcgctaacttcaattggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG
   |    |||  | ||||| ||   || ||||| |||  |  |     |  |   |    |  || || ||    |  |    |  || |  | | |||||||||| || ||  |||| || ||||||||||| |||||||| |||||||| |||||||| ||||| ||||| ||  | |||||| | ||||| |
-gttggctatttctacttcatactagttggaacactttgtgttgtttgttcctttctctttcgttgattatcatgtaagtttccttaattgcttgtctcagGCGAGGAGCCATTGTCACTACTTTCATTGTGTGTTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGAAATGGGG

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 8
taatacagattatttcttca-acacatttgaacaatttaagcagaagcataatcctttacacagtgtttttcgc-taacttcaattggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG
   |    |||  | ||||| ||   || ||||| |||  |  |     |  |   |  |    || || ||   ||| |||  |   || |  | | |||||||||| || |||||||| || ||||||||||| |||||||| ||||||||||||||||| ||||| ||||| ||  | |||||| | ||||| |
agttggctatttctacttcatactagttggaacactttgtgttgtttgttcctttctctcttgttgattgtcatgtaagttccttc--attgcttgtctcagGCGAGGAGCCATCATCACTACTTTCATTGTGTGTTATGCTCTCACATCTTTTATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGAAATGGGG

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
taatacagattatttcttcaacacatttgaacaatttaagcag------aagcataatcctttacacagtgtttttcgctaacttcaattggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG
||  || || |  | | |      | ||   | ||| |           | |   | | |||  | ||   || ||   ||||||   ||  ||| ||     ||| ||||| || ||  |||||||||||||||| ||||||||||| |||||||| |||||||| ||||| ||||| ||  | |||||| | ||||| |
tatcactgaatgctcccttcctctagttttcctattgactatatcttttatgtcaacttcttctcccatcattattatgtaactttccttcaatg-tg-----cagACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 8
-----taatacag-attatttcttc-----aacacatttgaacaatt--taagcagaagcataatcc-tttacacagtgtttttcgctaacttcaattggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG
     || ||||  ||| |||  ||     | ||  ||||     ||  |   |  |       |    ||  | | ||  ||| ||| || ||  ||        | | ||||| |||| || ||| ||||||| ||||| |||||||||||||| || |||||| | ||||| ||||| || |||||  | |||||||| |  || |
gtatgtattacactattcttttctcttgagaccaattttgtgttgttgttttccctacatgcggttggcttgtatattggattttgctcacctc--ttattctaattatttcagGAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGG

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|67012575|gb|CO441324.1|CO441324
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
EST: gi|9028738|gb|BE238778.1|BE238778
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
EST: gi|78079181|gb|DV507593.1|DV507593
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
EST: gi|21891548|gb|BQ744761.1|BQ744761
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
EST: gi|89249565|gb|DY621351.1|DY621351
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATT-GGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTT
EST: gi|13516079|gb|BG518355.1|BG518355
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTT
EST: gi|9028529|gb|BE238524.1|BE238524
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
EST: gi|71327794|gb|DR800533.1|DR800533
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
EST: gi|32931030|gb|CF035842.1|CF035842
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
EST: gi|67018280|gb|CO447029.1|CO447029
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
EST: gi|9953890|gb|BE640473.1|BE640473
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
EST: gi|94476145|gb|EB705103.1|EB705103
EST:     CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGG                         GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT
genomic: CTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTT

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: 48 (upstream exon), 48 (downstream exon)
Score: 206

GTTTGATGTTTCTTTCTGCACTTGTTGGTATCGGTACCCAATTGGCAGCTCTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 210

GTTTGATGTTTCTTTCTGCACTTGTTGGTATCGGTACCCAATTGGCAGCTCTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

GTTTGATGTTTCTTTCTGCACTTGTTGGTATCGGTACCCAATTGGCAGCTCTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG


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

GTTTGATGTTTCTTTCTGCACTTGTTGGTATCGGTACCCAATTGGCAGCTCTTATCCTACTTGTGATCGTTTTGGCCATCGTTGGCATGCTATACATTGGgtacactcaa ... tgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcataatcctttacacagtgtttttcgctaacttcaattggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG
                         cgctaac  putative branch site (score: 313)
                  tgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatacagattatttcttcaacacatttgaacaatttaagcagaagcataatcctttacacagtgtttttcgctaacttcaattggatggtgtttgtcagGCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - caacaca
- - - - - - - - - - - - - - gaacaat
- - - - - - - - - - - - - - - - - - - -gcagaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatgg