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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctaaaatgaattttaattttggacagagggagtatttatgatggcaagatattctggcaataagattgactgacaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG

Basic information

species Zea mays
transcript GRMZM2G078576_T04
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 15
----------------------------atctaaaatga----attttaatt-ttggacagagggagtatttatgatggc---aagatattctggcaataagattgactg-----acaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
                               | |||||       ||| ||  ||| |||         | | |||   |   || |||||||||      |||||| ||     ||||| ||   |||  | |||| ||||||||||| ||||| ||||||||||||||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| ||||| ||
gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggtgtccggattgattggcttgacaatatataatgatctgtttt-cagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG

upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA10G38920.2 (Glycine max), 3'ss of exon 15
atctaaaatg-aattttaattttggacagagggagtatttatgatg-gcaagatattctggcaa--taagattgactgacaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
   ||| ||| || | || |||| ||     ||  |  ||    || | || |   |  ||     |  |  |   |   |     || |   || ||| |||||||||||||||  |||| || |||||||| ||||| || || || ||||| || |||||||||||||  ||||  || || || || ||  |
--gtaagatggaaatatattttttgatttgtggtttgcttccagtgtggaataccattaggtggattttgtcttgtttctatgaggctgtatcttgtttgtcagATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTGCTATCCCGTTG

upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA20G28880.1 (Glycine max), 3'ss of exon 14
atctaaaatg-aattttaattttggacagagggagtatttatgatg-gcaagatattctggcaataagattgactga---caatgta-ctttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
   ||| ||| || | || |||| ||     ||  |  ||    || | || |   |  ||        ||| || |   | |||   || |   || ||| |||||||||||||||  |||| || |||||||| ||||| || || || ||||| || |||||||||||||  ||||  || || || || |   |
--gtaagatggaaatatattttttgatttgtggtttgcttccagtgtggaataccattaggtggattatttgtcttatttctatgaggctgtatcttgtttgtcagATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTTCTATCCCATTG

upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 15
lower sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 15
atctaaaatgaattttaattttggacagagggagtatttatgatggcaagatatt--ctggcaa--taagattgactgacaatgtactttgaatt---atttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
   ||||| | | ||   | |||  ||     |||  ||   ||      || ||  |||  |   || | |  ||| |  | ||| | | ||||    |||  ||||||||||| || || || || |||||||| ||||| ||||| || ||||| ||||||||||| ||||  ||||  || || || || ||  |
--gtaaaaggcaattggttgttgagcaattacagttgttccaattaatgaatcttatctgaaaggttatgttccacttatcacgtaatataaatttccgtttgacagATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTG

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|149083574|gb|EE172908.2|EE172908
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|87155515|gb|DY400304.1|DY400304
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGTGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|78111274|gb|DV529671.1|DV529671
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|166692487|gb|EG166994.1|EG166994
EST:     ATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: ATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|22472877|gb|BU037357.1|BU037357
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGTGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|24766669|gb|CA401816.1|CA401816
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCCCCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|37376751|gb|CF624930.1|CF624930
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|148945634|gb|EC890893.2|EC890893
EST:     TTGAAGTCATCAATAAAACTTCCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTATTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|166698538|gb|EG154852.1|EG154852
EST:     TGAAGTCATCAAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCC
genomic: TGAAGTCATC-AATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCC
EST: gi|93282383|gb|EB674647.1|EB674647
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTATTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA

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: 74

TCGAATGGACATGCAACAATTAGATGGGGAATGGTCCGTGGATAAAGTGCTTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

TCGAATGGACATGCAACAATTAGATGGGGAATGGTCCGTGGATAAAGTGCTTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

TCGAATGGACATGCAACAATTAGATGGGGAATGGTCCGTGGATAAAGTGCTTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TCGAATGGACATGCAACAATTAGATGGGGAATGGTCCGTGGATAAAGTGCTTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagatattctggcaataagattgactgacaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
                        gactgac  putative branch site (score: 134)
                                            ttatttttc  putative PPT
                               aatgtactttgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctaaaatgaattttaattttggacagagggagtatttatgatggcaagatattctggcaataagattgactgacaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG

- - - - - - - - - - - - - - - - - - - tatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttctggc