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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag

Basic information

species Zea mays
transcript GRMZM5G804893_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g38820.5 (Oryza sativa), 5'ss of exon 1
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgt---ccgctctttgcag-------------------
|||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||| ||| | ||  |  || |   | |   ||| ||||  |||         | ||   |  | ||   |  || |||||   || | |  |   ||||||||||  || |  || |    |||     | | ||||  |                   
TCATGAAGAAGGCCATCCCGGCCAACGGGAAGATCGCCAAGGACGCCAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACCAGCGAgtgagt-cgtcgccctcgtcctcccccctcttgtgctctgctctgctctgctctgtctt--cttttgagttttgagctt---tgagctcgttgtttgacttgtcgttggcggcgatgagatgtgactgggtttttgttgtggtggggcaacattacag

upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G36220.1 (Glycine max), 5'ss of exon 2
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttg---ttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag
|||||||||||||  | || || ||||| || |||||||||||||| || |||||||| ||||| ||||| ||||||||||||   |||||||| ||||||| |||| ||         ||   |||||   ||  ||  |||    ||      ||    |  | | | | ||||||  || |     ||||  |  ||                                       
TCATGAAGAAGGCACTACCTGCGAACGGTAAAATCGCCAAGGACGCCAAAGAGACCGTTCAGGAATGCGTATCCGAGTTCATCAGTTTCATCACCAGCGAgttagtgtctttttcttttctttttcttatgattcattctcttccgttttttctcttattatatcatcccgtgctttaatttcgaatccgtttaatcgtgtag------------------------------------

upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgc---ctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag
|||||||||||||  | || || ||||| || ||||| |||||||| || |||||||| ||||| ||||||||||||||||||  ||||||||| ||||||| ||||     |    | |  |||| ||||   |   |     || ||    ||        || || |    ||||   |  || |  || |||                                           
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgttagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaa---tttaaaattccttgaattctgtag-----------------------------------------

upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaa----tttggagtggcgttcagggctttagc--ttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag
|||||||||| ||  | ||  |||| || ||||| |  || || |||||||| || || ||||| |||||||| |||||||||  |||||||||||||||||| |     |   |         ||||  ||         ||||||| ||    ||||   |   ||  |     ||     || | |||   |||| |||                                        
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattcccaattt------ttcttctttcaatcgaatttgttggaaaatattttgctctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg------------------------------------

upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0004g03490.t01 (Vitis vinifera), 5'ss of exon 1
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgta--agtgcctcagctgcggctgactcttacttttgcttggcttg--ttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag
|||||||||||||  | ||||| ||||| |||||||||||||| || ||||||||  | || || ||||| ||||||||||||   |||||||| ||||||||  || |  |    |     || |  |  |  |   ||||||    ||||    |  ||      |  |    || ||      |     ||||  ||                                        
TCATGAAGAAGGCTCTTCCGGCCAACGGCAAGATCGCCAAGGATGCGAAGGAGACTCTCCAAGAATGCGTTTCCGAGTTCATCAGTTTCATCACCAGCGAgtatgagggttttgtttttaattgtcggt-gccgtaatttggctccgtttggtcgctgagaaaattttggaaaagttaagaggaattaaaactttgaattt---------------------------------------

upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag
|||||||||||||  | || || || || |||||||| ||||| || || |||| | |||| || |||||||| |||||||||   |||||||||||||||||  || || |        |   | ||| ||||    ||   ||     |||    |||  |||  ||  ||    ||   | || |     |                                          
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgta--tggctgatgcattttttctttttaattttaggcggtgcgt----gattgatggtgttgtt--ggttttgtttttcaattggatgcctag------------------------------------------

upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag
|||||||||||||  | |||||||| || |||||||||||||| || ||||| || || || |||||||||||||||||||||   |||||||| |||||||| | |  ||     |   |  || || ||| |  ||  |     |   |||  |  | | |||    | || |    || ||   | || |  |    | ||                                
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctcc----gatgattgtgttttgggttatttgattaaaa--ggatgaaatcttttccttctatttctc------------------------------

upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: EDP06643 (Chlamydomonas reinhardtii), 5'ss of exon 1
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcag----ctgcggctg------------actcttacttttgcttggcttgttgggaatt-tggagtggcgt----tcagggctttagcttggctggggttt-tgtgttgacttgtccatgtccacgtttttttg-tccgctctttgcag
| |||||||||||  |||||   |||| ||| || |||||||| || |||||||| || |||||||||||||| ||||||||   |||||||||    ||||||||| ||  |    | || ||||             | |   |  | ||       ||  |||    | |    ||       || | ||   ||   ||  |  |   ||||  |  |        || | | |  | || |  || || || ||
TTATGAAGAAGGCGCTCCCGAACAACGCGAAAATAGCCAAGGATGCAAAGGAGACGGTCCAGGAGTGCGTCTCGGAGTTCATTAGCTTCATCACGTCGGAgtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtag

upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ15374 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag
| |||||||||||  | ||||| || |  |||||||||||||| || |||||||| ||||| || |||||||| |||||||||  |||||||||||||||||||||    |  |      |     | |  ||  ||     |  |   | |||| ||                                                                              
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCGGAGTTCATCAGCTTCATCACTAGCGAgtaagtattgcttcgatcctttgtggtgatgttaact--atcttcttctactttgtag------------------------------------------------------------------------------

upper sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ24973 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag
| |||||||||||  | ||||| || |  |||||||||||||| || |||||||| ||||| || |||||||| |||||||||  |||||||||||||||||||||        ||| |     |||| |  |   |||   || |   |  ||    |    | |||                                                                    
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCAGAGTTCATCAGCTTCATCACTAGCGAgtaagtat------tgctggaagttctttcgatcctttgtggtgatactatcttcttctactttgcag--------------------------------------------------------------------

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|21809618|gb|BQ667936.1|BQ667936
EST:     GAGACCGTTCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGA                         AGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA
genomic: GAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA
EST: gi|18172372|gb|BM347760.1|BM347760
EST:     TGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGA                         AGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA
genomic: TGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA
EST: gi|26559930|gb|CA832165.1|CA832165
EST:     GAGACCGTTCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGA                         AGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA
genomic: GAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA
EST: gi|161593612|gb|EY964989.1|EY964989
EST:     GAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGA                         AGCGAGTGACAAGT
genomic: GAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGT

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: 153

TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 61

TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC