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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaggcacattcgttacttctcatctttgacatgcacaatgataattcatctaacatgttgtttggcaaaattttccacacttatttcctcaataagttctctattatgaaaaaataattttttggtttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG

Basic information

species Zea mays
transcript GRMZM2G037185_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g08480.1 (Oryza sativa), 3'ss of exon 5
gtaagtt-aggcacattcgttact---tctcatctttgacatgcacaatgataattcatctaacatgttgtttggcaaaattttccacacttatttcctcaataagttctctattatgaaaaaataattttttggtttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG
||||||| ||     || | || |   | || |||| || | |||  ||||| ||||||||    || | |      ||  ||||||  ||   ||      ||| ||||||| | |             ||   |  || |||||||||||||||||||||||| ||||||||||||||||||||||| || ||||||||||||||||| || |||||||| |||||||||||||||||||||||
gtaagtttagttgtgttagataatctctttcttcttggaaacgcatgatgatgattcatctcgtctgctctcac---aagctttccatgctctattttctggtaacttctctaatcta------------ttctatcactatgcagCATCTCTGCATATTGAATATCCTATGCTATTTGAAGTCCACAACGCGGCAGCAGAACGGACTTCACACTGTGGTGTCCTGGAGTTCATTGCAGAAGAAGG

upper sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G34630.2 (Glycine max), 3'ss of exon 5
gtaagttaggcacattcgttacttctcatctttgacatgcacaatgataattcatctaacatgttgtttggcaaaattttccacacttatttcctcaataagttctctattatgaaaaaataattttttggtttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG
                         | |  |||| ||||      | | |    | |   || ||| ||       | |||||  |  || |      | |||| || | |   || |        |  | ||  | ||||||||||||||||||||| ||||| ||| | |||||| |||  ||||  || || || |||  ||| |||||||| ||||||||||||||||| || |||||
------------------------gttagttttgtcatg------gttgaactgttttttattttgcttactt--ttattccaggcgaatatatatcttgagttttcaaattctaaca--------tcagtttaatttgcagCATCTCTGCATATTGATTACCCAATGTTGTTTGAACTCCGTAATGATGCTGCCGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCTGAGGAAGG

upper sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G01000.1 (Glycine max), 3'ss of exon 3
gtaagttaggcacattcgttacttctcatctttgacatgcacaatgataattcatctaacatgttgtttggcaaaattttccacacttatttcctcaataagttctctattatgaaaaaataattttttggttt--ctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCA-----GAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG
                         |  | |||    |  ||  ||||  |  || |||    |  | |  | ||  |||||||  | || |        | ||  | |  || | || |  | | |   || |     |||||||| ||| | |||||| || |||||| | ||| || ||   ||||  ||  ||     || |||  ||| |||||||| ||||||||||||||||||||      
-----------------------gttagttttt----taaactctgatcttatatttaatgcatgttct--ctaatctttccac--tgatgttgatgtccaattgacaaaaataacaagactaatgtccagtgtaatcttgcagCATTTCTACGTATTGATTATCCTATGATGTTTAAACTCAGAAATGGTGCTTCAATTCTGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCAGAT-----

upper sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G05030.1 (Glycine max), 3'ss of exon 5
gtaagttaggcacattcgttacttctcatctttgacatgcacaatgataattcatctaacatgttgtttggcaaaattttccacacttatttcctcaataagttctctattatgaaaaaataattttttggtttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG
                                      |     | ||  || | ||    | || ||| ||  | ||||  |  |    |   |  |||  ||     || | |||   |||  |   | ||  | ||||||||||||||||||||| ||||| ||| | |||||| |||  ||||  || || || |||  ||| |||||||| ||||||||||||||||| || |||||
----------------------------------gttagttttgtcatggttgaactgtttttttattttgcttactttt--attccaggtgaatatatagcttg--agttttcaaattctaacatcaagtttaatttgcagCATCTCTGCATATTGATTACCCAATGTTGTTTGAACTCCGTAATGATGCTGCCGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCTGAGGAAGG

upper sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G00980.1 (Glycine max), 3'ss of exon 4
gtaagttaggcacattcgttacttctcatctttgacatgcacaatgataattcatcta-acatgttgtttggcaaaattttccacacttatttcctcaataagttctctattatga-aaaaataattttttg-gtttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG
                                             | || ||  |  |  ||| || |||     ||| || | |||| || |        |  |  | |   | | || | |||| |   | ||     |||||||| ||| | ||| || || || ||| | |||||| ||   ||||  ||  | ||  ||  ||| |||||||| |||||||||||||||||||| |||||
---------------------------------------------gttagttttttaatgcatattcttt-----aatctttc-cactgatgttgatgtccaactgacaaaagtaacaagagtaatgtcgagtgtaatcttgcagCATTTCTACGTATGGATTATCCAATGATGTTTGAACTCAGAAATGGTGCTTCTGAGAGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCAGATGAAGG

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|18384255|gb|BM417454.1|BM417454
EST:     TTATAATGCCACCATCAGCTCTTGATCGTCTTG                         CATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
genomic: TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
EST: gi|211152115|gb|FL081689.1|FL081689
EST:     TTATAATGCCACCATCAGCTCTTGATCGTCTTG                         CATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
genomic: TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
EST: gi|71332942|gb|DR803495.1|DR803495
EST:     TTATAATGCCACCATCAGCTCTTGATCGTCTTG                         CATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
genomic: TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
EST: gi|93281779|gb|EB674043.1|EB674043
EST:     TTATAATGCCACCATCAGCTCTTGATCGTCTTG                         CATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
genomic: TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
EST: gi|18384443|gb|BM417642.1|BM417642
EST:     TTATAATGCCACCATCAGCTCTTGATCGTCTTG                         CATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
genomic: TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
EST: gi|87151920|gb|DY396709.1|DY396709
EST:     TTATAATGCCACCATCAGCTCTTGATCGTCTTG                         CATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
genomic: TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
EST: gi|18385079|gb|BM418278.1|BM418278
EST:     TTATAATGCCACCATCAGCTCTTGAACGTCTTG                         CATCTCTGCATATTGAATACCCTATGCTATTTGAAGACCACAATGCAGCAG
genomic: TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
EST: gi|22489686|gb|BU049609.1|BU049609
EST:     TTATAATGCCACCATCAGCTCTTGATCGTCTTG                         CATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCTCTATGCAGCAG
genomic: TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
EST: gi|71766016|gb|DR963953.1|DR963953
EST:     TTATAATGCCACCATCAGCTCTTGATCGTCTTG                         CATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG
genomic: TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAG

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: 44 (upstream exon), 49 (downstream exon)
Score: 256

TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 315

TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 291

TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 221

TTATAATGCCACCATCAGCTCTTGATCGTCTTGgtaagttagg ... ttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcctcaataagttctctattatgaaaaaataattttttggtttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG
                                    ttttttggtttctct  CT-rich tract
       tcaataagttctctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaggcacattcgttacttctcatctttgacatgcacaatgataattcatctaacatgttgtttggcaaaattttccacacttatttcctcaataagttctctattatgaaaaaataattttttggtttctctgcagCATCTCTGCATATTGAATACCCTATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG