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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatatttgctgaagacacttcctgacagataaccataagtagctctagctctgataattttatgtgttgttttctaatgtttgtattctggcttgctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA

Basic information

species Zea mays
transcript GRMZM2G410515_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 13
gtgaggatatttgctgaagacacttcctgacagata-accataagtagctctagctctgataattttatgtgttgttttctaatgt----ttgtattctggcttgctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA
||||||| ||||    |   | |  |||  | |||| | |||| |||| ||||      ||| ||  |||     || ||| | ||    || | ||||| ||  || | ||||||| |||||||| ||| ||||  ||||||| |||||||| ||||| ||||| ||||| || ||||| ||||||||||||||||| |||||||||||||||
gtgaggacattttgcaagagcgccccctatctgatatatcataggtaggtcta------atagttggatgcacacttctctcacgttcctttcttttctgtctcactgttacagATCTGTTTACAAGACTATCCCGGACTGTGAACCTTGCCGACCTCTGCAAAGATCACCGATTGAAGGGTTCTATCTAGCTGGTGACTACACAAAGCAGAAA

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 12
---------------------gtgaggat-atttgctgaagacacttcctgacagataaccataagtagctctagctctga--taattttatgtg----ttgttttct-aatgtttgtattctggcttgctttga--cagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA
                     | | |||| ||||  |  ||   |||    | ||||     |     |   | | | | |  ||| |    |||    |||| |||| |||  |  |      |  | | |||   ||| ||||||||||||||||| ||||| ||||| ||||| || ||  | ||||| || ||||| |||||||||||| ||||||| ||||||||||| || |||
gtttgattgaatacccacagagggtggattatttcttttagcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatttgtgttctgaatcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 12
------gtgaggatatttgctgaagacacttcc--tgacagataaccataagtagc---tctagctctgataatt--ttatgtgttgttttctaatgtttgtattctggct-tgctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA
       |||  |      |||   |    |    ||  |   |||     ||  |   | |||| || | | |    | |||  ||  | ||||||    ||  ||||||    | |  ||| || |||||||||||||| ||||| ||||| ||||| || ||  | ||||| || ||| | |||||||||||| ||||||| ||||||||||| || |||
gtttgattgaataaccagtctggcaatgtctttgttgttactgaactgatggtgacatttatagcccttacattcagctgtgttctgaatcctaatggaacta--ctggctacattgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAGATCTCCTTTAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 13
gtgaggatatttgctgaagacacttcctgacagataaccataagtagctctagctctgataattttatgtgttgttttctaatgtttgtattctggcttgctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA
|| ||   | |||    |   | ||     || || |     |  ||   |  |  |||||| || |    |  || |||| ||||             || |   |||||| || ||||| ||  ||||||||||||| || || || ||||| ||||| |||||||| ||||| |||||  ||||||| ||||||||||| ||||| 
gttagtgaagttgtaccatttatttagcttcaaatga--gggaccaggctttacattgataaattca-acatctttctctattgtt-------------gcatgatcagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 13
gtgaggatatttgctgaagacacttcctgacagataaccataagtagctcta-gctctgataattttatgtgttgttttctaatgtttgtattctggcttgctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA
  |    | ||| |       | ||  || |   | |   |   |   |     || | |||   |  |||  |  |||  |    ||| ||||   |||       |||||| |||||||||||||||||||| ||||| |||||||| ||  | ||||| || ||||| || || || ||| ||||||| || |||||||| || |||
--gttttttttttccacgtcaagttattgccttttgattttcgtttatttagtactattatagcatattgtaataattttaagctattggattc-aactt-------cagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA

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|211500355|gb|FL431278.1|FL431278
EST:     GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|16379611|gb|BI993047.1|BI993047
EST:     GTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: GTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|113704041|gb|EE681545.1|EE681545
EST:     TAAGTATCATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: TAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|211323425|gb|FL039625.1|FL039625
EST:     GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCCAACTGTGAGCCTTGCCGGCCTCTCCAA-G
genomic: GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|4573270|gb|AI586829.1|AI586829
EST:     CATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: CATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|211500354|gb|FL431277.1|FL431277
EST:     GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|89248324|gb|DY620110.1|DY620110
EST:     GATCAGAGTAAAGCAAAGATTTTTAAGTATCATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|13558607|gb|BG549963.1|BG549963
EST:     GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|4573271|gb|AI586830.1|AI586830
EST:     GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|71765382|gb|DR963319.1|DR963319
EST:     GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
EST: gi|31350094|gb|CD434451.1|CD434451
EST:     GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAG                         ATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG
genomic: GATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAG

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: 44 (upstream exon), 48 (downstream exon)
Score: 52

ATGCAACTATGGAAGAGCTAGCCAAGTTATTTCCTGATGAAATTGCTGCTGATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 149

ATGCAACTATGGAAGAGCTAGCCAAGTTATTTCCTGATGAAATTGCTGCTGATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

ATGCAACTATGGAAGAGCTAGCCAAGTTATTTCCTGATGAAATTGCTGCTGATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 65

ATGCAACTATGGAAGAGCTAGCCAAGTTATTTCCTGATGAAATTGCTGCTGATCAGAGTAAAGCAAAGATTCTTAAGTATCATATTGTGAAGACACCGAGgtgaggatat ... gctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgataattttatgtgttgttttctaatgtttgtattctggcttgctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA
                      ttctaat  putative branch site (score: 65)
                                          cttgcttt  putative PPT
     taattttatgtgtt  TA-rich tract