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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT

Basic information

species Zea mays
transcript GRMZM2G006130_T08
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 15
gttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
|||||| ||  ||  |   |     || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||||||||||| ||||| ||||| || |||||||||||||| |||||||||||||| ||||||||||||||  ||||| | || || ||||| || ||| ||
gttagttttgatgactccatggtttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCCTAGTTACTGGATGCAGACTCTTTTCGGTGAATCTAGCGGTGCTATGTTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 14
gttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
|||||| ||  ||| |   |     || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||||||||||| ||||| ||||| || |||||||||||||| || ||||||||||| ||||||||||||||  ||||||| || || ||||| || ||| ||
gttagttttgatggctccatggtttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
--gtta-gtattcttggtt----ttttttaccctctacttgttcttttcccgttgctc----taacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
  || | || || |   ||    | || |      |  |   || | | | |||| ||    | | | |    | |  |||| || |       |   | |||||||||||||| || ||||| ||||||||||  || | |||||||||||||||||| ||| ||||     |||||   |||||||| || || |   ||
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttc--tgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
-gttag-tattcttggtttt--ttttaccct--ctacttgttcttttcccgttgctctaac-----gctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
 || |  | || |   || |  | |||   |   ||||      | |    ||| ||   |     |||    | || |||| || |       |  || ||||||||||| || || ||||| ||||||||||  || | |||||||||||||||||| ||| ||||     |||||   ||||| || || || |   ||
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttc--tgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 16
gttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaa-----cgagatcagG-TGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
||  || | ||    ||||  |||      ||||   |  |       || ||        |  ||||   || | | |||      |  | | | | |||| ||| || || || |||||||| || |        |||||||||||||||||||||||||||    ||||| || | || || || || |   ||
gtatgtctcctca--ttttcctactaaaaccttgccttcattatacatctatacttaaatcaatatttaaatttggaaaaattttctctcgttaaagCTGGAGCCCAGATGCAATCGTCTTCAATTCTTCCTTTGTGTATGGAACTCCTAGCTACTGGATGCAGCACTTTTTCAGCAACTCCAGTGGAGCGACTCTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
-------gttagtattcttggttttttttaccctctacttgttcttt----tcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
       | |     || |  | |   |        || | |   ||    |   |  |     | |||| ||  |   |   | |        | || ||| |||||||| || || ||||||||||||||||||||||| ||||| || || ||||||||| | ||     |||||    | || | |||||||    | 
tacagaaggtgaaggtcatcatatccctcgtggaacacgtatgaattgaaatgaagaggaatgtaagctgagaaaac--tagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC

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|211495379|gb|FL350690.1|FL350690
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211098336|gb|FL317177.1|FL317177
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211378660|gb|FL357038.1|FL357038
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211258110|gb|FL346334.1|FL346334
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|18654846|gb|BM499651.1|BM499651
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211474807|gb|FL320108.1|FL320108
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC

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: 179

TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 764

TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 492

TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 343

TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
            ctctaac  putative branch site (score: 343)
                            attttgttt  TA-rich tract