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

gtacagttgaatgtttgcaaaatggatctcataactccaggctggcttatctcaataatcactttttttcctgttgtgatgtgacgtgggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATTGTGGGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGA

Basic information

species Zea mays
transcript GRMZM2G013750_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 3'ss of exon 8
gtacagttgaatgtttgcaaaatggatctcataactccaggctggctta--tctcaataatcactttttttcctgttgtgatgtgacgtgggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATTGTGGGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGA
            ||  |  |  | | | |||  | | ||   |  | |   | | |||  ||  | |  |||||  | |    ||    |  || || |||||| |||||||||| || || ||||||||||| || |||||||||   ||||||||||||| |||  | |||| ||  || ||||||||| | || |||
------------gtacgttatgttgctttcaggattacaaattatcatggtttttaatgttctttctaattcctacttttgc-tgtttggatgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTTGTGGGAATTCTTTAAAGATGAATATGCGAATGAGAAGAATTTTCTCGGA

upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 8
gtacagttgaatgtttgcaaaatggatctcata-actccaggctg-gcttatctcaata--atcactttttttcctgttgtga-tgtgacgtgggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATTGTGGGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGA--
       |   |  |   ||  |  ||||||   | |||| |    | | || |   ||  ||  | || |    || ||||  ||| |  ||  |     |||||| |  |||| |||||||||||||||||||| ||||| |||||  |  | |||||    | ||||   || ||||| || ||||||   |  || |||  
------gtatgttatcctaacttttatctcacgtattccaagtcatgttcattttcttaggatttccttgtcatttggtgtgcctgttatatgttgtgcctagGTTACTTTTGAAACAGCTGGTTACCATGGAGGTTATCCAATGGACCACTCTATGGGATACATATAAGAGTGATTTTGAGAATGAGAAGG--CCTCTGGGAAA

upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 8
gtacagttgaatgtttgcaaaatggatctcataactcc--aggctggcttatctcaata--atcactttttttcctgttgtga-tgtgacgtgggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATTGTGGGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGA--
       |   |  |   ||  |  ||| |||   | |  || |  | | || |   ||  ||  | || |    || |||   ||| |  || | |   | || || |  |||| |||||||||||||||||||| ||||| |||||| |  | |||||    | ||||   || ||||| || ||||||   |  || |||  
------gtatgttctcctaacttttatcccatgttttccaagtcacgttcatttgtttaggatttccttgtcatttggtgtacctgttatatgtgtgccta-gGCTACTCTTGAAACAGCTGGTTACCATGGAGGTTATCCAATGGACAACTCTATGGGATACATATAAGAGTGATTTTGAGAATGAGAAGG--CCTCTGGGAAA

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|6194444|gb|AW146548.1|AW146548
EST:     CAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGTTTT
genomic: CAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|78545102|gb|DV622600.1|DV622600
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|60394675|gb|DN227545.1|DN227545
EST:     AGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: AGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|5847143|gb|AW000222.1|AW000222
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|37377438|gb|CF625322.1|CF625322
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|60345832|gb|DN212805.1|DN212805
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|60396663|gb|DN229531.1|DN229531
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|149074395|gb|EE162783.2|EE162783
EST:     CCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|67021450|gb|CO450199.1|CO450199
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|37400251|gb|CF637475.1|CF637475
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|60349290|gb|DN216263.1|DN216263
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|60358924|gb|DN225897.1|DN225897
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|211414360|gb|FL328790.1|FL328790
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|211088675|gb|FL328946.1|FL328946
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGT
EST: gi|78023300|gb|DV491687.1|DV491687
EST:     CAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
EST: gi|33095588|gb|CF055582.1|CF055582
EST:     CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAG                         GTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT
genomic: CTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATT

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), 47 (downstream exon)
Score: 275

TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCGAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATTGTGGGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCGAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATTGTGGGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCGAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATTGTGGGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 296

TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCGAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttga ... ggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATTGTGGGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcttatctcaataatcactttttttcctgttgtgatgtgacgtgggggaaaaagGTTATTGCTGAAGCAGCTGGTTACCATGGAGGTCATCCAGTGGACAGCATTGTGGGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGA
          aataatcacttttttt  TA-rich tract