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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcctcgtcacctccgtcagctttcgccttctttcttccgttagttcgttccctcgctcgttcggtcactcacattcgcgtccgttggttcgatcgacgacggcgaccgcgcgcgctcgcttgtctgtttgccagGGTGCTGTCCAACTTCGCATTCTCCTTCTCCATCATCTCGGTGCTGACGGGGGTCACGACGCTCTACAACACGGGGCTCAACTTCGGCGGCCCCGCCACC

Basic information

species Zea mays
transcript GRMZM2G013456_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013456_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g42234.2 (Oryza sativa), 3'ss of exon 1
gtacgttcctcgtcacctccgtcagctttcgccttctttcttccgttagttcgttccctcgctcgttcggtcactcacattcgcgtccgttggttcgatcgacgacggcgaccgcgcgcgctcgcttgtc--tgtttgccagGGTGCTGTCCAACTTCGCATTCTCCTTCTCCATCATCTCGGTGCTGACGGGGGTCACGACGCTCTACAACACGGGGCTCAACTTCGGCGGCCCCGCCACC
                                         | |||     |  | || | |||  ||  || ||| | | |   | ||    ||   | |  |||    | |  |  | | |||  | |   |     ||| ||||||||||||||||| ||||| ||||||||||||||||||||||||||| |||||||||| |||||||||||||||| ||||||||| || ||||||
----------------------------------------gtacgtcgccacactgcccctctctctctctctctctcgtcccttttcgcccttttcttggctgactttaaaccggttcacgcgcgcgacggcggcgtgcagAGTGCTGTCCAACTTCGCCTTCTCGTTCTCCATCATCTCGGTGCTGACGGGGATCACGACGCTGTACAACACGGGGCTCAGCTTCGGCGGGCCGGCCACC

upper sequence: GRMZM2G013456_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g42234.1 (Oryza sativa), 3'ss of exon 1
gtacgttcctcgtcacctccgtcagctttcgccttctttcttccgttagttcgttccctcgctcgttcggtcactcacattcgcgtccgttggttcgatcgacgacggcgaccgcgcgcgctcgcttgtctgtttgccagGGTGCTGTCCAACTTCGCATTCTCCTTCTCCATCATCTCGGTGCTGACGGGGGTCACGACGCTCTACAACACGGGGCTCAACTTCGGCGGCCCCGCCACC
                                  | |   ||   |||            |   |    |  |   |||   |   | |  ||    |||  |||  |    | |   |   |  || |  |  ||| ||| ||||||||||||||||  | || ||||| ||| | ||||||||||||||| |||||||||| | |   ||||||||  | |||||||| || || || 
---------------------------------atttcattttttttaaaaaaaaaagagggaggaaaagaaatgaacaaaggaaacag--gg---aatcagcgaaaggtgtcac-tactgacaatttttggcgtgc-agGCTGCTGTCCAACTTCGCGGTGTCGTTCTCGATCGTGTCGGTGCTGACGGGGATCACGACGCTGTTCGGGACGGGGCTGCAGTTCGGCGGGCCGGCGACG

upper sequence: GRMZM2G013456_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S47_191V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacgttcctcgtcacctccgtcagctttcgccttctttcttccgttagttcgttccctcgctcgttcggtcactcacattcgcgtccgttggttcgatcgacgacggcgaccgcgcgcgctcgcttgtctgtttgccagGGTGCTGTCCAACTTCGCATTCTCCTTCTCCATCATCTCGGTGCTGACGGGGGTCACGACGCTCTACAACACGGGGCTCAACTTCGGCGGCCCCGCCACC
                                      | | |  ||  |      |  |      |||  | |   ||     |   |    ||  ||   |      ||||  |  |    |||||  | | | |||| ||  | || |||||||||||||||||| ||||||||||  | || || ||  |||||||| | | ||||||||||||||| |  |||||  | | | | 
------------------------------------agtatccaattcttggaaagctacagaatgtcg--cgcctgcacgtaagcttgaatattttattatctgtaatgacca-gttcttgtgcttgatt-tataccagAGTTTTATCGAACTTCGCATTCTCCTTCGCCATCATCTCCATACTCACAGGAATCACGACGTTGTTCAACACGGGGCTCAATTATGGCGGAACAGTCTCT

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 2 RNA-Seq libraries.


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

CCGGTGGCGGCAGCGCCGTGACCGTCGACCACAGTGACGACACCGGCCTGGCGCGCTTGCGGGAGCTCGGGTACAGGCAGGAGCTGAAGCGCGACCTCTCgtacgttcct ... tgtttgccagGGTGCTGTCCAACTTCGCATTCTCCTTCTCCATCATCTCGGTGCTGACGGGGGTCACGACGCTCTACAACACGGGGCTCAACTTCGGCGGCCCCGCCACC


Block sizes: 42 (upstream exon), 18 (downstream exon)
Score: 2

CCGGTGGCGGCAGCGCCGTGACCGTCGACCACAGTGACGACACCGGCCTGGCGCGCTTGCGGGAGCTCGGGTACAGGCAGGAGCTGAAGCGCGACCTCTCgtacgttcct ... tgtttgccagGGTGCTGTCCAACTTCGCATTCTCCTTCTCCATCATCTCGGTGCTGACGGGGGTCACGACGCTCTACAACACGGGGCTCAACTTCGGCGGCCCCGCCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgttggttcgatcgacgacggcgaccgcgcgcgctcgcttgtctgtttgccagGGTGCTGTCCAACTTCGCATTCTCCTTCTCCATCATCTCGGTGCTGACGGGGGTCACGACGCTCTACAACACGGGGCTCAACTTCGGCGGCCCCGCCACC
                                       cttgtct  CT-rich tract