Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcatgttcactgtatcagtaacataattcacacgctttgtttccttacatgatttattgtttagtttccagaatgagacattatcatgcgtttagcacctcaaatttgggacataatctttattcgtgttaattcctctcaacgattttcattttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT

Basic information

species Zea mays
transcript GRMZM2G147721_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 5
gtaagatcatgttcactgtatcagtaacataattcacacgctttgtttccttacatgatttattgtttagtttccagaatgagacattatcatgcgtttagcacctcaaatttgggacataatctttattcgtgttaattcctctcaacgattttcattttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT
                                                   |  |  ||   ||||    ||| ||  ||   |  ||||      |||||||  ||| | |||||  || ||||| |||        ||| | | |  ||    ||| |||  ||||| ||||| ||| |||||||||||||||||||| || ||||| || ||||| 
---------------------------------------------------tctagaatgagttgt---atttgcactat---attttat------tttagcagttcagaattgggttatgatcttcatttaatggtgttcttttaactga----catattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 6
gtaagatcatgttcactgtatcagtaacataattcacacgctttgtttccttacatgatttattgtttagtttccagaatgagacattatcatgcgtttagcacctcaaatttgggacataatctttattcgtgttaattcctctcaacgattttcattttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT
                                                  ||  |||    ||| | ||  |||||   |   |  || |      |||    | |     |||| |          ||  ||  ||||  ||  |||  ||   |||  |   ||| |  || |  || |||||||||||||| || || ||||||||||||||||| 
--------------------------------------------------tttgatg--caattttatatattccactttagtatcttgttcactatttctttcttt---cttggaa----------atcagtactaatgactagcaa--atggacatcatctgcagGCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCCA

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 6
gtaagatcatgttcactgtatcagtaacataattcacacgctttgtttccttacatgatttattgtttagtttccagaatgagacattatcatgcgtttagcacctcaaatttgggacataatctttattcgtgttaattcctctcaacgattttcattttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT
                                                          || | ||   | |||     ||   || | |  ||    ||  ||  |    | |       ||     ||   |  ||||  ||  |||  |    ||| ||   ||| |  || |  || |||||||||||||| || |||||||| ||||||||||| 
----------------------------------------------------------ttcaatg--caattttatatattccacttcagtatcttgttcacaatttctttctttattggaa-----atcaatactaatgactagcaa--acggacatcttctgcagGCATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCG

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 6
gtaagatcatgttcactgtatcagtaacataattcacacgctttgtttccttacatgatttattgtttagtttccagaatgagaca-ttatcatgcgtttagcacctcaaatttgggacataatctttattc--gtgttaattcc---tctcaa-cgattttcattttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT
                                                              |   | ||  | || |  | ||   || |  |   ||    ||    ||||| |     | | ||| |||  |||||  ||     | ||||  | || |  ||     ||||| ||||| ||| ||||||||||| || |||||||| |||||||||||||| 
-------------------------------------------------------------gtaagtgagaattcaaatagtgattcttgttttattttacttacaatcaattttgattccatttttttttcttgtgtttcttttaattatcaagtggttgtgtttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA

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|148986684|gb|EE030466.2|EE030466
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|60355786|gb|DN222759.1|DN222759
EST:     AAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: AAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|148995918|gb|EE035161.2|EE035161
EST:     CTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: CTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|148972761|gb|EE023734.2|EE023734
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCCCATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|149102315|gb|EE188183.2|EE188183
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|149081093|gb|EE170194.2|EE170194
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|148986685|gb|EE030467.2|EE030467
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|71437045|gb|DR818095.1|DR818095
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|148943253|gb|EC888314.2|EC888314
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|74235474|gb|DT643388.1|DT643388
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
EST: gi|111189546|gb|EE287682.1|EE287682
EST:     ATCCCTCCCCACGAGGGGGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCC

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), 48 (downstream exon)
Score: 23

GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagatcat ... ttttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggacataatctttattcgtgttaattcctctcaacgattttcattttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT
                    tgttaat  putative branch site (score: 69)
                                       ttttcatttt  putative PPT
      ataatctttatt  TA-rich tract