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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgtagtagtagctactagctagctagctgctgctagctccctggcccggtcgctcgtcttggttctgatcgtttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG

Basic information

species Zea mays
transcript GRMZM2G052544_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052544_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g07770.1 (Oryza sativa), 3'ss of exon 1
gtacgtgtagtagtagctactagctagctagctgctgctagctccctggcccggtcg--ctcgtcttggttctgatcgtttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG
|||||  |  |   | ||   |   |  |  || |    |  ||          |    ||| ||||  ||  |||   ||  |     | |      |||||||||||| |||||||| ||||||||||| |||||||| ||||| || |||||||||||||||||||||||||| |||
gtacgcatcatca-atctctcaatcaattctctccaaaaaaatcgaaacaagaattaatctcttctttcttacgatgaattgatgatcgtcttgtcgtcgcagAGGCGACGCCCAAGACGATCATGAGGGTGATGGGAGTGAAGGGCCTCACCCTCTACCACCTCAAGAGCCATCTCCAG

upper sequence: GRMZM2G052544_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G29620.1 (Glycine max), 3'ss of exon 1
--gtacgtgtagtagtagctactagctagctagctgctgctagctccctggcccggtcgctcgtcttggttctgatcgtttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG
    |  |  |  || |     |    |  |||    | |  |    |  |     |   || | || ||     || || | |    || | |     |||||||| ||||| || || ||||||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||||
aataaaatagaaaagcaaaaggtgttaatttagtgtattcatgtgttcatgtattattattc-ttttagtaac--tctttcctttgtgttctatgatttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG

upper sequence: GRMZM2G052544_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G17400.1 (Glycine max), 3'ss of exon 1
gtacgtgtagtagtagctactagctagctagctgctgctagctccctggcccggtcgctcgtcttggttctgatcgt-ttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG
|| | ||||| |  |   | ||      |||    |          |||         |  ||||     | ||| | ||  || ||||||       |||||||| ||||| || |||||||||||||| ||||| || ||||| || ||||| ||||||||||||||||| || |||
gttcttgtag-accaaaaattattgtattagaca-tatgtctatgttggatgatattatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG

upper sequence: GRMZM2G052544_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G41740.1 (Glycine max), 3'ss of exon 1
-gtacgtgtagtagtagctactagctagctagctgctgctagctccctggcccggtcgctcgtcttggttctgatcgtttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG
 |||     |  |     || ||  |   ||  |   | |       ||| |     | || | |   |  | ||| ||| |||  ||||    |   |||||||| ||||| || |||||||||||||| ||||| || ||||| || ||||| ||||||||||||||||| ||||||
tgtagaccaaaaatgtagtagtacatgtttatgtttggattatattatggtctcaatgatcttttgattaatcatctttttctcttttttggattt--gcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAG

upper sequence: GRMZM2G052544_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S25_131V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacgtgtagtagtagctac-tagctagctagctgctgctagctccctggcccggtcgctcgtc-ttggttctgatcgtttcctccctttttctctcac---gcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG
       |  |  |  |||  | | |||  |  || |      ||   ||    ||     ||| |     || |    |   ||  | ||  || ||     ||||||| || || ||  |  | ||||| ||||||||||| ||||| ||||| || |||||  | |||||||||||||||
-----gatgttgctgactaagttggtagtaaaatg-tatgtcttcgtgggattagtattaggtcatcaaaactaactcgtctgtcattgttgttcacaatggacagAGGCTACACCGAAATCTGTAATGAGAGTCATGGGAGTGAAGGGTCTTACTCTTTACCATTTGAAGAGCCATCTTCAG

upper sequence: GRMZM2G052544_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S201_75V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtacgtgtagtagtagctactagctagctagctgctgctagc--tccctggcccggtcgctcgtcttggttctgatcgtttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG
 |  | | |  |   || |  | |     ||| || |   | |  | | | |    |  |  |  ||   |   | | || |         |   || ||  |||||| || || ||| |  | |||||||| |||||||| ||||| ||||| ||||||||  | ||||||||||| |||
tgggcttctgctgagagatgatcggagtgtaggtgatctaaacgattcgtagtgacgaagtccaactc--tctcgtttgtctgtggtgaaatcaactgac--agAGGCTACACCGAAGTCTGTGATGAGGGTTATGGGAGTGAAGGGTCTTACGCTCTACCATTTGAAGAGCCATCTCCAG

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 20 (downstream exon)
Score: 10

GGCCTCGTCCTCACCACCGACCCCAAGCCCCGCCTCCGCTGGACCGTCGAGCTCCACGAGCGCTTCGTCGACGCCGTCACGCAGCTCGGTGGCCCCGACAgtacgtgtag ... tctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 25

GGCCTCGTCCTCACCACCGACCCCAAGCCCCGCCTCCGCTGGACCGTCGAGCTCCACGAGCGCTTCGTCGACGCCGTCACGCAGCTCGGTGGCCCCGACAgtacgtgtag ... tctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 17

GGCCTCGTCCTCACCACCGACCCCAAGCCCCGCCTCCGCTGGACCGTCGAGCTCCACGAGCGCTTCGTCGACGCCGTCACGCAGCTCGGTGGCCCCGACAgtacgtgtag ... tctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcccggtcgctcgtcttggttctgatcgtttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG
                                            ctctcac  putative branch site (score: 17)
               tcttggttctgatcgt  CT-rich tract
                                       tttttct  TA-rich tract