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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattttcttcacttaaagctgtttcacatgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT

Basic information

species Zea mays
transcript GRMZM2G102475_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102475_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g49520.2 (Oryza sativa), 3'ss of exon 8
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattttcttcactta--aagctgtttcaca-tgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATT-CTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT
||  |||| || |||||||||| ||| ||| ||   |||   |||  | | ||   |||  || | | |  ||     ||   ||  || | ||| | |    |||   ||  ||| ||| ||| |   ||   ||  ||||| |||||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||| | || || |||||    |  | |||||||||||    ||  | 
gtcgctttacttctttgcatcattctgcaccttttttta--tccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactctttt-atgaactggtc--ttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCA-AATCTTGATGTTTGATGTTCATAGGG

upper sequence: GRMZM2G102475_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G05410.5 (Glycine max), 3'ss of exon 8
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattt-tcttcacttaaagctgtttcacatgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATT-CTAATTGTATG-----CAGACCTGATGT---TTGATAACTATTAGT------------------------
                         ||  |  |   ||  ||   |||||   |||   |||   |||  |  ||  |    ||||     |      | || |||| | |    | ||||  |||   || |  || || ||||||||||||||||| || ||||||||||||||||||||| ||| || | |     |||||||  || ||  |  | ||      ||    || |    ||||| |||    ||                        
------------------------gtttgccct--tttcaactgtaaactaataatgggcatgagtctatagcta--gtcccttcaagaact------ggaaatctattat---atctgat--atcaaataatg-ctctgctctgcaggttatttttaattttggtccaaaagtgtccatattcacattttattcagacgaagataagtttctgttcatgtgaattgtagTGTCGAAGCAACTTGATGACTGGATGTTTCCTGCTAATTGCAGGATTTTAG

upper sequence: GRMZM2G102475_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G05410.4 (Glycine max), 3'ss of exon 8
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattt-tcttcacttaaagctgtttcacatgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT--
                         ||  |  |   ||  ||   |||||   |||   |||   |||  |  ||  |    ||||     |      | || |||| | |    | ||||  |||   || |  || || ||||||||||||||||| || ||||||||||||||||||||| ||| || | |     |||||||  ||    ||  |||  ||  ||  || |   | | | | |   
------------------------gtttgccct--tttcaactgtaaactaataatgggcatgagtctatagcta--gtcccttcaagaact------ggaaatctattat---atctgat--atcaaataatg-ctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTT-CATGT-GAATTGTAGTGTCGAAGCAACTTGATG

upper sequence: GRMZM2G102475_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G19640.2 (Glycine max), 3'ss of exon 8
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattttcttcacttaaagctgtttcacatgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT-
                                    ||   |     |  || || |        ||     || ||||  | |     || | | | |     | || |    | ||||  |||   || |  || || ||||||||||||||||| || ||||||||||||||||||||| ||| || | |     |||||||  ||    ||  |||   |    |   ||||      ||  | 
----------------------------------gtttgcccttttcaactgtaagctaatgggcctgagtctatagctagtcc----cttcaagaactggacat-ctattatatctgat--atcaaataatg-ctatgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTT-CATGTGAATTGTAGTGTTGAAGCAACTTGATG

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|261490328|gb|GO359834.1|GO359834
EST:     TTGTACATTCAGTGGACTGAGCATCATAAAAGGCTGTCCAATTTCTTAAG                         GTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGG
genomic: TTGTACATTCAGTGGACTGAGCATCATAAAAGGCTGTCCAATTTCTTAAGgtaactttgc ... tgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGG
EST: gi|67015111|gb|CO443860.1|CO443860
EST:     ATTTCTTATA-                         GTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAG
genomic: ATTTCTTA-AGgtaactttgc ... tgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAG

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), 48 (downstream exon)
Score: 521

CGCTCCGCGCTCGTGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTGTACATTCAGTGGACTGAGCATCATAAAAGGCTGTCCAATTTCTTAAGgtaactttgc ... tgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

CGCTCCGCGCTCGTGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTGTACATTCAGTGGACTGAGCATCATAAAAGGCTGTCCAATTTCTTAAGgtaactttgc ... tgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

CGCTCCGCGCTCGTGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTGTACATTCAGTGGACTGAGCATCATAAAAGGCTGTCCAATTTCTTAAGgtaactttgc ... tgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 222

CGCTCCGCGCTCGTGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTGTACATTCAGTGGACTGAGCATCATAAAAGGCTGTCCAATTTCTTAAGgtaactttgc ... tgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT
                     gtttgat  putative branch site (score: 222)
                                      ttttctgt  putative PPT
                                 tgttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattttcttcacttaaagctgtttcacatgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA