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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagacactaacttattgtatctgagtacttcccttaatcttgtctgttgctaatatcatcatcttcaatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG

Basic information

species Zea mays
transcript GRMZM2G701689_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g41230.2 (Oryza sativa), 3'ss of exon 6
gtaagagacactaacttattgtatctgagtacttcccttaatcttgtctgttgctaatatcatcatcttcaatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG
||||||| ||||  |||  | |  ||   |   ||| ||  |     ||  |||| |||| ||| | | | ||||| |||||   ||| || ||||||||||||||  ||||||||||||| || |||||||| |||||||| || ||| | ||||||||||| ||||||| ||||
gtaagagccactctctttgttttacttcctttctcctttgttacgtgctactgctcatataatcct-tgctatattatagGATGACTCTAACAAAACTCCTGCTTCTTCTCGTCACAAAAGAGGCTGCAATTGTAAGAAGTCATCGTGTTTGAAAAAATACTGCGAATGTTATCAG

upper sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
---gtaagagacact-aacttattgtatctgagtacttcccttaatcttgtctgttgctaata-tcatcatcttcaatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG
     || | | |||  ||||| | | ||     |        ||  |  | | | | || || | || |||||     ||||||||   | | ||||||||||| |||||||| || |||||||| |||||||| ||||| || ||    || ||||| ||||| |||||||||| ||||
gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttataggtattaattattatcttt----ttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG

upper sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
gtaagaga--cactaacttattgtatctgagtacttccc-----ttaatcttgtctgttgctaatatcatcatcttcaatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG
|| ||  |   | ||  | | | ||| |    |||| |      | || | | | | || |  |||| |     ||     ||| ||||   | | || |||||||| |||||||| || |||||||| ||||| ||||||||||| ||    || ||||| ||||| |||||||||| ||||
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG

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|50331744|gb|CO526870.1|CO526870
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|87156415|gb|DY401204.1|DY401204
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|26559555|gb|CA831790.1|CA831790
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|31359966|gb|CD444323.1|CD444323
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|31349638|gb|CD433995.1|CD433995
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|32932451|gb|CF037263.1|CF037263
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|31357841|gb|CD442198.1|CD442198
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|20512944|gb|BQ280130.1|BQ280130
EST:     CATTTGCTCCTAATGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|76915167|gb|DV165860.1|DV165860
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|7162203|gb|AW519825.1|AW519825
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
EST: gi|22715536|gb|BU197816.1|BU197816
EST:     CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGG                         GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT
genomic: CATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAAT

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: 335

GGAAACTGTTCTATCTACGCGGCAACAGATTGAATCTCGCAATCCATTAGCATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

GGAAACTGTTCTATCTACGCGGCAACAGATTGAATCTCGCAATCCATTAGCATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG


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

GGAAACTGTTCTATCTACGCGGCAACAGATTGAATCTCGCAATCCATTAGCATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

GGAAACTGTTCTATCTACGCGGCAACAGATTGAATCTCGCAATCCATTAGCATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagaca ... aatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtacttcccttaatcttgtctgttgctaatatcatcatcttcaatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG
                          tgctaat  putative branch site (score: 233)
                             taatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagacactaacttattgtatctgagtacttcccttaatcttgtctgttgctaatatcatcatcttcaatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT