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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgcttaaattcttggactggttcaagcgcttgctctatctcttccctttactttggttcaagcgcttggccgcttgcgctatctcttttccttttagtttggctatctctgttgatctggaataagtagatattgtgttaacattgtcttttacaatgtgctcttctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT

Basic information

species Zea mays
transcript GRMZM2G124051_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g07080.1 (Oryza sativa), 3'ss of exon 11
gttagtgcttaaattcttggactggttcaagcgcttgctctatctcttccctttactttggttcaagcgcttggccgcttgcgctatctcttttccttttagtttggctatctctgttgatctggaataagtagatattgtgttaacattgtcttttacaatgtgctcttctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT
                                                                            | ||| | |    ||||   ||  | |   ||      ||| | ||||||||| | | ||||||     | |||  | ||| || |||  | ||| |||||||||||||| ||  | || || || ||  |||| ||  ||||||||||||||||  | |||||||| || |||||||| |||||||||||||| ||||||||
----------------------------------------------------------------------------gtttgtggtgaaactttg--ttgaaatgctgcctgtggtgt-gttctggaatatgcaaatattgct---agatttacctttgcattgtatt-ttccatttcagCGGATTCGTTATCAGTGGAATCGTTGCTGGAACTTCTGGATGAGGATAGCTTACGGAAAGACACTGCGCTTCCTTCACCTGAATGGTCATCAGATCATAT

upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 10
gttagtgcttaaattcttggactggttcaagcgcttgctctatctcttccctttactttggttcaagcgcttggccgcttgcgctatctcttttccttttagtttggc--tatctc-tgttgatctggaataagtagatattgtgttaacattgtcttttaca-atgtgctcttctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT
                                                                                                  | ||  |||   ||| || | |||||    |  |  |   |||  |||| ||| | |  |  | | || ||   |    |||||||||||||||||  ||| ||||||||||||||| || |||||||||| || ||||| || ||||| || |||||||| ||||||||||| || ||||| ||
-------------------------------------------------------------------------------------------------gtgagcatggtgttatatcattttgataaacataatatctgtatcttgttcacaattttatgaagagatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTGCTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT

upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
gttagtgcttaaattcttggactggttcaagcgcttgctctatctcttccctttactttggttcaagcgcttggccgcttgcgctatctcttttccttttagtttggctatctctgttgatctggaataagtagatattgtgttaacattgtcttttacaatgtgctcttctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT
                                                                                           |   | |   |||     || |   |  |  |  ||||  |  || ||| || |   || | |   |  || ||   |    |||||||||||||||||  ||| ||||||||||||||| |  |||||||||| || ||||| || ||||| || |||||||| ||||||||||| || ||||| ||
------------------------------------------------------------------------------------------gtgagcatggtgttatatcattttgataaactt--aatatctgtatcttg-gtcacatttttatgaaaagatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT

upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 10
gttagtgcttaaattcttggactggttcaagcgcttgctctatctcttccctttactttggttcaagcgcttggccgcttgcgctatctcttttccttttagtttggctatctctgttgatctggaataagtagatattgtgttaacattgtctttta--caatgtgctcttctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT
                                                                                          | |    | | |    | ||| ||  || || ||  | || |  | ||  || | | ||||| | | |    ||    | |    |||||||||||||||||  ||| |||||||| |||||||| ||||||||||| || ||||| |||||||| || |||||||||||||||||||| || ||||||||
-----------------------------------------------------------------------------------------gtgtgatatcttgcaatgttatgtc-attaatttgata-aatttaacatcctgatca-attgtttatgaagtgataccttttgtgttttcagCGGATTCATTGGTTGTGGAGTCATTGTTGGAGCTATTGGATGAGGAAAGTTTGAGGAAAGACACAGCACTTCCTTCTCCTGAATGGTCCTCTGATCATAT

upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA19G39210.3 (Glycine max), 3'ss of exon 10
gttagtgcttaaattcttggactggttcaagcgcttgctctatctcttccctttactttggttcaagcgcttggccgcttgcgctatctcttttccttttagtttggctatctctgttgatctggaataagtagatattgtgttaacattgtcttttacaatgtgctcttctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT
                                                                                          | |    | | |    | ||| ||  || || || ||||| |  | ||  || | || |||| | | |     |    |    |||||||||||||||||  ||| ||||||||  ||||| | ||||||||||| || ||||| |||||||| || |||||||||||||||||||| || ||||||||
-----------------------------------------------------------------------------------------gtgtgatatcttgcaatgttatgtc-attaatttg-aataatttaacatcctgatcac-ttgtttatgaagtgatatcttgtgttttcagCGGATTCATTGGTTGTGGAGTCATTGCTGGAGTTATTGGATGAGGAAAGTTTGAGGAAAGACACAGCACTTCCTTCTCCTGAATGGTCCTCTGATCATAT

upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 10
gttagtgcttaaattcttggactggttcaagcgcttgctctatctcttccctttactttggttcaagcgcttggccgcttgcgctatctcttttccttttagtttggctatctctgttgatctggaataagtagatattgtgttaacattgtcttttacaatgtgctcttctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT
                                         |||| || |||  |  | ||||   ||   |      ||   |||| | || |      |  |     ||   ||| | |   |      | ||| ||    ||  ||| |||  || |||  | | |    || |||| || || || || || || ||||| ||||| || ||||||||||||||||||||||||||||| || ||||||||||| || ||||| || ||||||||
--------------------------------------gtaatctttttcctacatgtcggttt--gcatct------ttttcctatattttatttacacatgtgcttcatacttgtagtttgtgccgttattgatgtt----taggattctctaata-aataagatttgtggttccagCCGACTCTTTAACGGTGGAATCATTGTTGGAACTCTTGGATGAGGATAGCTTGAGAAAAGACACAGCACTTCCTTCTCCGGAGTGGTCCTCTGATCATAT

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|91049453|gb|EB159871.1|EB159871
EST:     AAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAG                         CGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCT
genomic: AAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAGgttagtgctt ... tctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCT
EST: gi|211089863|gb|FL154003.1|FL154003
EST:     AAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAG                         CGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCT
genomic: AAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAGgttagtgctt ... tctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCT
EST: gi|24767403|gb|CA402546.1|CA402546
EST:     AAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAG                         CGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCT
genomic: AAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAGgttagtgctt ... tctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 53

GATCACCAGCGAAGGAGGATGGACCCTGGGACAAATGAGCCATTGTTCACAAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAGgttagtgctt ... tctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 55

GATCACCAGCGAAGGAGGATGGACCCTGGGACAAATGAGCCATTGTTCACAAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAGgttagtgctt ... tctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 91

GATCACCAGCGAAGGAGGATGGACCCTGGGACAAATGAGCCATTGTTCACAAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAGgttagtgctt ... tctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 24

GATCACCAGCGAAGGAGGATGGACCCTGGGACAAATGAGCCATTGTTCACAAATTGCACAAGGGATTTTACCGGTACCCTAGATTACATATTTTACACAGgttagtgctt ... tctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaataagtagatattgtgttaacattgtcttttacaatgtgctcttctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT
                tgttaac  putative branch site (score: 24)
                                       tgctcttctatttc  putative PPT
                             ttttacaat  TA-rich tract