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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacattttttgaccactatgctattcagttgttgctaggctatctttctagtggtgtctagtttcttactcttgttttagGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG

Basic information

species Zea mays
transcript GRMZM2G089484_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 3
gtatgacattttttgaccactatgc--tattcagttgttgctaggctatctttctagtggtgtctagtttcttactcttgttttagGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG
||| | |||||   | ||||||  |  ||| ||| |  |        |  ||| ||       ||| ||  ||  |||  |||||||||||| ||||||| ||||||||||||||||||||| ||||||||||||| |||||||||
gtacgtcatttcacgcccactacacactatgcagctcattactcttaagatttatatcatcagctaattgatttttctgtttttagGATTATATTGCAACAAGGTGGTACCGAGCACCAGAGCTGTGTGGATCTTTTTTCTCCAAG

upper sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 2
gtatgacattttttgaccactatgctattcagttgttgctaggctatctttcta--gtggtgtctagtttcttact-cttgtttt-----agGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG
   | | | | |||  || ||    || |||  |    |   ||| || |  |    |  ||  | |||| |  |  |||||||      ||||||| |||||||| ||||||||  |||| || || ||||||||||| || |||||||||
--gtaagaatcttttgcctctgaaatactcaccttcaacatagctttcctcttgtcatcatgcattgtttatgcccacttgtttccttgcagGATTACGTTGCAACAAGGTGGTATAGAGCTCCTGAATTGTGTGGATCCTTTTTCTCCAAG

upper sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 3
gtatgacattttttgacc---actatgctattcagttgttgctaggctatctttctagtggtgtctagtt---tcttact-cttgttt-----tagGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG
||||||   |||||  |    |||||    |||| |||  ||   ||| |||||||       ||| ||    ||||| |  ||||||      |||||||||||||||| ||||||||  | || || |||||||||||||| || || ||||||
gtatgaatctttttccctgaaactatctccttcaattga-gcatagctctctttctcagttcatctcgtcacctcttaatgtttgtttgcttgcagGATTATGTTGCAACCAGGTGGTATAGGGCTCCTGAGTTGTGTGGATCCTTTTTTTCCAAG

upper sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 3
gtatgacattttttgaccactatgctattcagttgttgctaggctatctttcta--gtggtgtctagtttcttact-cttgtttt-----agGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG
   | | | | |||  || | |   || |||  |    |   ||| || |       |  ||  | |||| |  |  |||||||      |||||||||||||||| ||||||||  |||| || || ||||||||||| || |||||||||
--gtaagaatcttttgcctccaaaatactcaccttcaacatagctctcctctcgtcatcatgcattgtttatgcccacttgtttccttgcagGATTATGTTGCAACAAGGTGGTATAGAGCTCCTGAATTGTGTGGATCCTTTTTCTCCAAG

upper sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------------gtatgacattttttgaccactatgctattcagttgttgctaggctatctttctagtggtgtctagttt--cttactcttgttttagGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG
                                                                 |  | | | || |  |    ||    ||   ||| |  ||| |  || | |||||   || |   |||   ||  | |  ||  |||||||||||||||| ||||||||| | ||||| || |||||||| || || |||||||||
gtatgcttcttccccatttgtgtgtgtttcttgtcaatcaattgcaatggtctatttttctttgtgacttaaagttgtgtatgggtaaataatgatgtt-tccctatga-atatctctagaattgacagctttaatttcatgtgattacagGATTATGTTGCAACAAGGTGGTACAGGGCACCTGAATTGTGTGGTTCATTTTTCTCCAAG

upper sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ38694 (Selaginella moellendorffii), 3'ss of exon 3
gtatgacattttttgaccactatgctattcagttgttgctaggctatctttctagtggtgtctagtttcttactcttgtttt-----agGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG
                                     |  ||   |||   | |  | ||   | | ||| |||||  ||||     ||||||||||||| ||||||||||||||||| || ||  | ||||| || ||||| ||||||
-------------------------------------gtaagtgcatcaaacaaaggatggaca-tatctgactctcctttttttcaagGATTATGTTGCGACTAGGTGGTACCGAGCCCCCGAACTATGTGGCTCCTTCTTTTCCAAG

upper sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ31453 (Selaginella moellendorffii), 3'ss of exon 2
gtatgacattttttgaccactatgctattcagttgttgctaggctatctttctagtggtgtctagtttcttactcttgtttt-----agGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG
                                     |  ||  ||||   | |  | ||   | | ||| |||||  ||||     ||||||||||||| ||||||||||||||||| || ||  | ||||| || ||||| ||||||
-------------------------------------gtaagtgtatcaaacaaaggatggaca-tatctgactctcctttttttcaagGATTATGTTGCGACTAGGTGGTACCGAGCCCCCGAACTATGTGGCTCCTTCTTTTCCAAG

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: 143

AAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAATGATACTCCAACCGCCATCTTTTGGACGgtatgacatt ... cttgttttagGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 57

AAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAATGATACTCCAACCGCCATCTTTTGGACGgtatgacatt ... cttgttttagGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

AAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAATGATACTCCAACCGCCATCTTTTGGACGgtatgacatt ... cttgttttagGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 65

AAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAATGATACTCCAACCGCCATCTTTTGGACGgtatgacatt ... cttgttttagGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttgttgctaggctatctttctagtggtgtctagtttcttactcttgttttagGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG
                                     ttcttac  putative branch site (score: 65)
                                    tttcttactcttgttt  CT-rich tract
                                              ttgtttta  TA-rich tract