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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacgtgttgagctactgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG

Basic information

species Zea mays
transcript GRMZM2G073498_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 6
-taacgtgttgagctactgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
 |||  |        ||| |||| ||| |  ||        ||||| | | |  |||||| |  ||||| | | |   | |  ||  | |  |||   ||||| |||||||||||||||||||| ||||||||||| || || ||||| ||| ||||| |||||||||| || |||||||||||||||||||| ||||| |
gtaaaataaaacaaaactattttctatat--ctggtctggaatgcagaattatcatgcaagagctacctttaaac---caccaacctttgcaatttaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCGAATTTACAGAAAGAATTGAACAGATACATCCCTACAGCTGCTGCATTTGGTGGAGTCTGCATTG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 6
taacgtgttgagctac-tgttttatatttggctcactaatta--tgcaaactcactatgc-aacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
| |  ||   |   |  ||| ||| |  |  |  || ||| |  || |     | ||||    ||| |     || |||   |   ||| |    |   ||||||||||||||||||| ||||| ||||| |||||||||||||||||||| || ||||| |||||||| |||||||| || |||||||| ||  | || || |
tcatatggaaattcatatgtatta-agatatcagacaaataaactgtatctctattatgttggcaaattttgttggtcacggt---acatttttgaacttgcagGAACAACAAATGGTAATGCCCGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAATCGATACATTCCCACTGCCGCAGCATTTGGAGGCATCTGTATTG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 6
-taacgtgttgagcta-ctgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
 | |  |    |   | |||| ||| |  |  |  || ||| |     |   | ||||   |  | |  | || |  ||     ||| |    |   ||||||||||||||||||| ||||| ||||| |||||||||||||||||||| || |||||||||||||| ||||| || || |||||||| ||  | || ||||
atcaaatagaaattcatctgtattaaagataccagacaaatgaactttatctattatgt--cggtaaattttggtggtcacaatacatttttgaacttgcagGAACAACAAATGGTAATGCCTGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAACCGATACATTCCCACGGCCGCAGCATTTGGAGGCATCTGTATCG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G17950.1 (Glycine max), 3'ss of exon 6
---taacgtgttgagctac---tgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
   ||   ||| ||   |    ||   |  |  |   |   |  ||||  ||| |     ||| | |||     ||  |  |  | |     |   || | ||||||||||||||||||| ||||| |||||||| ||||||||||||||||| ||||||||||||||||| |||||||| || |||||||| ||  |||| || |
ctgtagtttgtagaaaaatccatgggctggacctatttttttgcttattaaaatttctgttgctataat-----gtatttcttgtttt-tgttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACTGCCGCAGCATTTGGAGGCATATGTATTG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
taacgtgttgagctactgttttatatttggctcactaattatgcaaactcactatgcaaca-atta--cctgtgatcatc-ctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
  |  | |  || |  |||  ||   ||      || | |     ||   | ||||      ||||    |  | |  || || |     |   || | ||||||||||||||||||| ||||| |||||||| || |||||||||||||| ||||||||||||||||| ||||| || || |||||||| ||  |||| ||||
--atatttgtagtt--tgtagtaagattcatgagctcaatgcctgaatctattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 5
taacgtgttgagctactgttttatatttggctcactaattatgcaaactca--------ctatgcaacaattacctgtgatcatcctctgacactg----gatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
     ||||    |  || |     ||   || |  ||   |||  |  ||        || ||   |  || | ||     | |   | |   ||    ||| || | |||||||| |||||||| ||||| || || || || |||||| | || |||||||||||||||||||| ||||| ||||| || ||||||||  | || ||||
--gtatgtttgtttgttgatcacccttgttctaagcaaagttgcggatccaattcttatctttgggtcttttgcatgactataactcttaaatttgtgttgatttttttcagGAACAGCAAATGGTAATGCCTGGTCACCGAGACTCAAACCTTCAAAAGGAACTGAACCGATACATTCCCACGGCTGCAGCTTTTGGTGGTCTGTGTATCG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0551g00030.t01 (Vitis vinifera), 3'ss of exon 3
taacgtgttgagctactgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctgaca----ctggat-attctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
   |  | |     |  |     ||||||  | ||  ||||||||     | |||  ||  |||   | || |   | || ||      || ||| ||| | ||||| ||||||||||||||||| || || || ||| | ||||||||||| ||||| || || ||||| |||||||| || || || || ||  | |||||||
-ttcacggttcataaaggaaaactatttgtttaac--attatgcatgtagattat--aaggattgattatggtggccatcagatgaattcttgatgatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAACTCAATCGCTACATACCCACTGCAGCAGCCTTCGGGGGTATGTGCATCG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 6
taacgtgttgagctactgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctga--cactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
|| | |    |  |  |      |||       |   ||||||   | |   | |  |   |  |   |||  ||||   |||     ||   ||| | ||||||||||||||||||||||| || ||||| ||| | ||||||||||| || || || || ||||| ||||||||||| || || || ||  | || ||||
taccatacgaatttgtttagcagtatg-aatatatagattatgaggaatatttgt-tagttacaattggtggccatcagttgaatttttgatgatttttcagGAACAACAAATGGTGATGCCTGGGCATCGGGAGGCCAACTTGCAGAAAGAGCTAAATCGCTACATACCCACTGCTGCAGCCTTCGGGGGTATGTGTATCG

upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------taacgtgttgagctactgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
                   | |  ||  | |  | |||  |    || |    | ||||| |   | |   |      |  | |  |   |     ||| | | ||     ||   ||||||||||||||| | ||||| || || ||||| || ||| | |||| |||| ||||||| ||||| ||||| || ||||| ||||| ||  | || || |
gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG

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|211338834|gb|FL045911.1|FL045911
EST:     GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAG                         GAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacag ... tattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAA
EST: gi|166491200|gb|EG075753.1|EG075753
EST:     GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAG                         GAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAAC
genomic: GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacag ... tattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAAC
EST: gi|71425883|gb|DR806950.1|DR806950
EST:     GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAG                         GAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacag ... tattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAA
EST: gi|211338836|gb|FL045913.1|FL045913
EST:     GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAG                         GAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacag ... tattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAA
EST: gi|31354346|gb|CD438703.1|CD438703
EST:     GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAG                         GAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacag ... tattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAA

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: 462

GTTTTATGTGGTCTTCATGCTGTCAGCTTGCGCTCTGTTCTCAAAAACGTGGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacag ... tattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

GTTTTATGTGGTCTTCATGCTGTCAGCTTGCGCTCTGTTCTCAAAAACGTGGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacag ... tattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 286

GTTTTATGTGGTCTTCATGCTGTCAGCTTGCGCTCTGTTCTCAAAAACGTGGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacag ... tattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 695

GTTTTATGTGGTCTTCATGCTGTCAGCTTGCGCTCTGTTCTCAAAAACGTGGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacag ... tattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcactatgcaacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
            aacaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacgtgttgagctactgttttatatttggctcactaattatgcaaactcactatgcaacaattacctgtgatcatcctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG