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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT

Basic information

species Zea mays
transcript GRMZM2G053004_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g27960.1 (Oryza sativa), 3'ss of exon 3
gtatgttctttggtcccatgcc-gtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
|||||| ||||  |    | || || |||||||| |         |  ||||||||  |||   | | ||           ||||||||  || |||||             || || ||||||||||||  |||||||||| ||||| ||||| || || |||||||| ||  | |||||| ||||||| |||||||| || ||||||||||| || ||
gtatgtgctttcattttgtacctgtcctatcttttc---------attcaaatcttggcttcgtcggatg-----------gtaaagattcaaacttttctg----------aactgcagTTGGGGGGCTGTTGAATGCTACCTTTGGCAATGCGACTGAGATGATTATCTCGTTGTACGCATTGAAAAACGGGATGATCCGTGTCGTCCAGCAATCGCT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
                          ||||  || |       ||      | ||    |||    | |  |  | ||||          |||    |    || |  |||    | ||||||||| || || ||||| || ||||| |||||||| ||||||||||||||||| || ||| ||||||     |||||  |||| || ||||| || ||
-------------------------gtatccctctt------ttatttccctttttctcttaaggcccgtatcctctttt---------caactcactcgtgttgctttct----gcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
          |   | |||    |  | | |||| |   |   | | ||     |  ||||  | |||          | || |  ||  |||    |||  ||   ||    ||| ||||||||| || || ||||| ||||| || |||||||| ||||||||||||||||| || ||| || |||     |||||  |||| || ||||| ||  |
---------gtatcctcat-ttattttctttttcttttcctatttatcattctctccctttgtctgct----------tcgtca--attcaactcacttctgttcatat----ttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S21_141V6.2 (Physcomitrella patens), 3'ss of exon 4
gtatgttctttggtcccatgccg-tgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
               | |||    |  ||     | | | | | ||| || ||   ||   |      | |||| |||| | ||  || |        ||  |||| |||    ||  |||||| || || |||||||| || ||||||||||| ||||||||||| ||||  |||   ||  |    ||    ||||| || || || |||   || ||
--------------tcaatgtgaattgtaagcacctttaacagataa-cagattcgaatgatctgttatacttattattat-tatcgaggatgttgactttatttttcat----ttccagTTGGAGGTCTCCTGAATGCGACTTTTGGAAATGCGACGGAAATGATCATATGCATAATGGCGTTACGGAAGAAAATGATACGAGTTGTACAGTTATCTCT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S245_10V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------gtatgttctttggtcccatgccgtgctatctttcctaagcggcta-agcaaatcttaac--tttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
                                 | |   | || | ||  || || ||| ||||   ||       |  || ||| |  |||  |||          |  | | |||  || | ||||||||| |        | ||   || |||||| || || |||||||| || |||||||||||||| ||||||||||| |  ||    || |||   ||    ||||| || || || |||   |||||
gtatttgctgacgctaaaccctcgcagcattgtgaagcatgttcgatcgaataccttgcaatctgagcttcattcttgtaggaaaacaaaacattttgctgatctagttctctcttgctaaaaagtaacctttgtg-------acctttgtgcagTTGGAGGTCTCCTGAATGCAACTTTTGGAAATGCAACTGAAATGATTATTTGTATCATGGCCCTGCGGAAGAATATGATACGAGTTGTACAGTTATCACT

upper sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
     |  |||       |  || |  ||         | || | |   |     | ||       ||   |     |  |  ||    |    ||||||           | ||| |||||| || || |||||||| || ||||| ||||||||||||||||||||||  ||    ||  |    ||    ||||| || || || |||   |||||
-----taatttaagttgttaacgggtaatggga---gggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttc-----------acttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT

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: 40 (upstream exon), 48 (downstream exon)
Score: 52

GCAACTTGCTTGCTACACTGGCCCAACAGgtatgttctt ... ctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT


Block sizes: 40 (upstream exon), 44 (downstream exon)
Score: 41

GCAACTTGCTTGCTACACTGGCCCAACAGgtatgttctt ... ctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78

GCAACTTGCTTGCTACACTGGCCCAACAGgtatgttctt ... ctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT


Block sizes: 29 (upstream exon), 48 (downstream exon)
Score: 50

GCAACTTGCTTGCTACACTGGCCCAACAGgtatgttctt ... ctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
                                           atctaat  putative branch site (score: 50)
                            cctttttccttttcca  CT-rich tract
      ttagtattttgtaaa  TA-rich tract