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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGATTCTGATTACTGGCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAACgtatccttgataatcattcattaagctggtttaaaatcatctgttctgttatgtagttgttacagcttgatgttcttaacattaaaaataaaagaagcgcag

Basic information

species Zea mays
transcript GRMZM2G041701_T02
intron # 13
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041701_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g33430.2 (Oryza sativa), 5'ss of exon 12
ACGGATTCTGATTACTGGCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAACgtatccttgataatcattcattaagctg--gtttaaa--atcatctgttctgttatgtagttgtt-acagcttg-atgttcttaacattaaaaataaaagaagcgcag----------
|| ||| |||||||||||||| || |||| |||||||| ||||| ||||||||||||||||||| |||||||||| || ||| |||||||  ||   ||||  |  ||     ||| ||||  | |||  ||   | |||  | ||   ||   ||  || |  ||| |    |           
ACTGATGCTGATTACTGGCTCATATCAGAAGGGGATGTCAGCATTACTGATATGTGGAAAACAGCACgtatcctttatgatcgttcattacacttttgtttggactattcatagttttgtttagaagtcatttgtaacttataagtagctactgttgcaacttgaagtacttaacatggaaacag

upper sequence: GRMZM2G041701_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA12G09860.1 (Glycine max), 5'ss of exon 13
ACGGATTCTGATTACTGGCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAACgtatccttgataatc--------attcattaagctggtttaaaat--catctgttctgttatgta----------------gttgttacagcttgatgttcttaacatt-----aaaaataaaagaagcgcag------------------------------------
|  ||  |||||||||||||  || |||| |  ||||||||||| ||||| ||||||| |||||||||||| ||   ||| |        || ||||    |  || || ||  |||    ||| |     |                | | |   ||  | || || ||   |||     ||||| || || |    ||                                    
AGTGAAGCTGATTACTGGCTTTTATCAGATGCTGATGTTAGCATAACTGACATGTGGAGAACAGAACgtattctctctaaactccttgacatccatttcattctttaaatatatcatgcactctatctcacacacacaaggagggaggggtttggaagtgtcatttttttttaatttttttaaaaaaaataggaatctaggcttgatgttcttaaacttccttgttacatttacag
















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|60347462|gb|DN214435.1|DN214435
EST:     GCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAAC                         TGGGATGAGATGGATTTCTTGTCAGAAGATGTTGTCACCC
genomic: GCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAACgtatccttga ... agaagcgcagTGGGATGAGATGGATTTCTTGTCAGAAGATGTTGTCACCC
EST: gi|60397671|gb|DN230487.1|DN230487
EST:     GCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAAC                         TGGGATGAGATGGATTTCTTGTCAGAAGATG
genomic: GCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAACgtatccttga ... agaagcgcagTGGGATGAGATGGATTTCTTGTCAGAAGATG

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: 45 (upstream exon), 44 (downstream exon)
Score: 13

ACGGATTCTGATTACTGGCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAACgtatccttga ... agaagcgcagTGGGATGAGATGGATTTCTTGTCAGAAGATGTTGTCACCC


Block sizes: 32 (upstream exon), 42 (downstream exon)
Score: 11

ACGGATTCTGATTACTGGCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAACgtatccttga ... agaagcgcagTGGGATGAGATGGATTTCTTGTCAGAAGATGTTGTCACCC


Block sizes: 40 (upstream exon), 44 (downstream exon)
Score: 7

ACGGATTCTGATTACTGGCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAACgtatccttga ... agaagcgcagTGGGATGAGATGGATTTCTTGTCAGAAGATGTTGTCACCC


Block sizes: 40 (upstream exon), 38 (downstream exon)
Score: 12

ACGGATTCTGATTACTGGCTCCTAACAGAGGGGGATGTTAGCATGACTGATATGTGGAAAACAGAACgtatccttga ... agaagcgcagTGGGATGAGATGGATTTCTTGTCAGAAGATGTTGTCACCC