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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG

Basic information

species Zea mays
transcript GRMZM2G009030_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 4
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaa--aacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
                                                          | || || | |||  |   |  |      ||  | ||||    ||  | | |||| | || |||||||||  | |    | | || ||         |  |||| ||||| || || ||||| |||||||||||||||||| |||||||||| ||||||||||||||||||||||| ||||||||||||||||| ||||| ||||| |
---------------------------------------------------------gtaccatcaaattcctattgttcttctgataatgatcagttctaagtccaatataaacatggactgcaaaatgacaaaaatatattcaa---------ctgtttttcagGTTAATCAAATTGGCACTGTCACTGAATCAATTCAAGCTGCTCTTGATTCAAAAGCTGCTGGTTGGGGCGTGATGGTCAGCCACAGGAGTGGGGAAACGG

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 3
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
                                                         |  |     | ||  || | |     || ||| | |||   | |||  |  ||   ||||| |  ||  ||  || | |||  |    |   |  ||     | ||||| |||||||||||||| || || ||||| ||| | ||||| || || ||||| ||||| |||||||||||  |||| || ||  | ||||| || || |
------------------------------------------------------aaacaccaactgaatttacagctt----gcttcaagatagttgttggctgaatttacagttgcaat-taatgcttcatttgttttgtgttgtccattgac-----tgcagGTTAACCAGATTGGTACAGTGACCGAATCTATTCAGGCTGCACTTGACTCAAAGGCTGCAGGTTGGGGTGTAGTGGTTAGTCATCGGAGTGGCGAGACTG

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 4
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgca-ctgcaaa-actaaatgtctttgttaaaattggtgtaccttt-ttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
                                                                     ||| | ||  |  | |  || ||    |  |  | | | | |  || || ||| ||  | | | |   || |||     || | | |  |   | ||||| ||||| |||||||| || |||||||| ||| | ||||| || || ||||| ||||| ||||||||||| ||||| || ||  | ||||||||||| |
------------------------------------------------------------------gcatcttatcaaaactaatcaaacaccagctgcatgttg-gctgaatttacagctgtaattaatgattcctttggttttttctgttatccaatgactgcagGTTAACCAAATTGGTACAGTGACTGAATCTATTCAGGCTGCACTTGACTCAAAGGCTGCAGGTTGGGGTGTCATGGTTAGTCATCGGAGTGGTGAAACTG

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 5
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtaccttt-ttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
                                                         |  |     | ||  || | |     ||  || | |||   | |||  |  ||    |||| |    || |    || | | ||     || ||| | ||   | ||||| |||||||||||||| || || ||||| ||| | ||||| || || ||||| ||||| ||||||||||| ||||| || ||  | ||||| || || |
------------------------------------------------------aaacaccagctgaatttacagctt----gctttaagatagttgttggctgaatttacagctgcaat---taattcttcgtttgttttg----tgttgtcctttgactgcagGTTAACCAGATTGGTACAGTGACCGAATCTATTCAGGCTGCACTTGACTCAAAGGCTGCAGGTTGGGGTGTCATGGTTAGTCATCGGAGTGGCGAGACTG

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
                       ||||  |    | ||||      ||||| | ||   |  |  || ||||| | | |||     ||||||      ||  | ||||  |  ||              ||| | |||||   ||||  ||     |||  ||||| ||||||||||| || |||||||| |||||| |||| || || || ||||||||||| || |||||||||||||| || ||||| ||||| || || |
-------------------gtaaaaataaaagtttttatatt----attttctcttttctaatctcaattctctagaccattttgacaaaacccccgtta-ttggagaagaatttc-------------aatttgtttgt---aattcatgg----tttcacagGTTAACCAGATTGGGACAGTCACTGAGTCAATTCAAGCAGCACTTGACTCAAAAGCTGCAGGCTGGGGTGTGATGGTTAGTCACAGGAGTGGCGAGACAG

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
                                                       |  || ||   | || |       |||  ||   | ||  || |  |   |   ||  || || ||   | |   || | | | |||| |||     |  |  || ||||| |||||||| || || || |||||||| ||| ||||||| || || || |||||||| || ||||||||||||||||| ||| | ||||||||||| |
-------------------------------------------------------tagttactggtaattgtt----ctatggttg---atcatcatatctcctaatgaaatatttca-tgttgatcctgatct-tatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S76_97V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattgg-tgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
                 |  |||    |   | | | |   |   |  || | || ||| | ||  |  |||   | | |    |  | ||   | | |   |  || | |  ||  |     ||| ||||||||||  ||     |   |||| |      ||||| || || || ||  |||| || || || ||| ||||||| || ||||| || || || ||||||||||| |||||||||||| ||||||| || || |
---------------gtatgctgtt-cgtgattccagaagacaccagattatgttagctccatttta--tcttcgctttaaatttagagaatgctgtttta-tgaagctca--ttaaagcatgaaagtaaatgtcttcattttttctaactgtatcgc---gcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTG

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ26490 (Selaginella moellendorffii), 3'ss of exon 5
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
                                                                                        || ||   | | ||     || |  |  ||  |  || | ||   | ||| ||    ||  | |  |||||| ||||| || ||| | ||  | || |||||||| ||  |||| ||| | ||||||||||||||||| |||||||| ||||| |||||||||||||| || ||||
--------------------------------------------------------------------------------------gtaagcacggtgtcgccttccatcatttctcatgg--aatcgaatccttttttttttcttttctttcgctttttgcagGTGAATCAGGTCGGCTCCGTGACTGAATCCATCCAAGCAGCTTTGGATTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCG

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ26799 (Selaginella moellendorffii), 3'ss of exon 4
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
                                                                                        || ||   | | ||     || |  |  ||  | | |   ||   | ||| ||    ||  | |  |||||| ||||| || ||| | ||  | || |||||||| ||  |||| ||| | ||||||||||||||||| |||||||| ||||| |||||||||||||| || ||||
--------------------------------------------------------------------------------------gtaagcacggtgtcgccttccatcatttctcatggaatag--aatccttttttttttcttttctttcgctttttgcagGTGAATCAGGTCGGCTCCGTGACTGAATCCATCCAAGCAGCTTTGGATTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCG

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|32866424|gb|CF006106.1|CF006106
EST:     GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTCAAGCTGCTCTCGATTCA
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
EST: gi|166692797|gb|EG322464.1|EG322464
EST:     GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAAACCAGATTGGTAC
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAA-CCAGATTGGTAC
EST: gi|76290554|gb|DV030122.1|DV030122
EST:     GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
EST: gi|22819501|gb|BU499591.1|BU499591
EST:     GTATAGCAGATGCTATTGATAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTCAAGCTGCTCTCGATTCA
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
EST: gi|76011516|gb|DT938686.1|DT938686
EST:     GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
EST: gi|33102792|gb|CF062752.1|CF062752
EST:     GTATAGCAGATGCTATTGATAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTCAAGCTGCTCTCGATTCA
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
EST: gi|149004756|gb|EE039253.2|EE039253
EST:     TATAGCAGATGCTATGGACAAGAAGGCTTGCAATGCTTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
genomic: TATAGCAGATGCTATTGACAAGAAGGCTTGCAATGC-TCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
EST: gi|76290528|gb|DV030096.1|DV030096
EST:     GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
EST: gi|7135894|gb|AW498320.1|AW498320
EST:     GTATAGCAGATGCTATTGATAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTCAAGCTGCTCTCGATTCA
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
EST: gi|87156544|gb|DY401333.1|DY401333
EST:     GTATAGCAGATGCTATTGATAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTCAAGCTGCTCTCGATTCA
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA
EST: gi|6020507|gb|AW065435.1|AW065435
EST:     GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAG                         GTCAACCAGATTGGTACTGTCACTGAATCAATTCAAGCTGCTCTCGATTCA
genomic: GTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCA

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: 68

AGTTGATATCCAAATTGTGGGTGATGATTTACTCGTCACAAACCCAAAACGTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 57

AGTTGATATCCAAATTGTGGGTGATGATTTACTCGTCACAAACCCAAAACGTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

AGTTGATATCCAAATTGTGGGTGATGATTTACTCGTCACAAACCCAAAACGTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 416

AGTTGATATCCAAATTGTGGGTGATGATTTACTCGTCACAAACCCAAAACGTATAGCAGATGCTATTGACAAGAAGGCTTGCAATGCTCTGTTGCTAAAGgtaaccattt ... ctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG
               aactaaa  putative branch site (score: 416)
                                          tacctttttcc  putative PPT
                        tctttgttaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattggtgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT