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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcatttattctggatctgacttttcacttctctttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC

Basic information

species Zea mays
transcript GRMZM2G056393_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 10
-------------------------------------------gtacgcagacaaacaaggggacaatct-tactttattttatagttctgtttacttcatttattctggatctgacttttcacttctctttg--tcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC
                                           ||||        || |    || || |   |||   |||   |||    ||     |||| |||||  |  | ||  | | || |  | |  |||||||| ||||||||||| |||||| ||||||||||||| |||||||| |||||||||||||||||||||||||||||||| || || |||||||||||||| ||
gtaaatttttgagtgaagtgtagggccacaggctattcaagaagtacctctgtccactatactaccatgtgctcttcgattttctgttgacattttcggatttgttctgtgttggtctgattatttgttctcgcatcaatagGTGATACATTTACAGATGGATCAGTGAAATATACCATGACTTCCATGAATGTCCCTGAACCTGTGATGTCCTTGGCTGTCTCCCCTATATCTAAAGATTC

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 10
----------gtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcattt--attctggatctgacttttcacttctctttgtcaat-agGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC
           ||  |      ||  ||   | | ||||   || |||     |||    |    | |   ||  ||  | |    ||      || ||  | ||| ||| |||||||||||||||||| |||| || || || ||||| || ||||| || ||||||||||| |||||||| || |||  |||  | || ||||| ||
gtacagtaaaatattcttgtgtacttggtt-cgaacttaacataatttgcttctctagggatgaaagtctgatattgtgtttcttgttgggtcacttttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTC

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 10
--------gtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcattt--attctggatctgacttttcacttctctttgtcaat-agGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC
          |           |   |  | | ||||   || |||     ||||   |    |||   ||  ||  | ||   ||       | ||  | ||| ||| |||||||||||||||||| |||| || || || ||||| || ||||| || ||||||||||| |||||||| || |||  |||  | || ||||| ||
gtacagtaaaatattcttccgtacttgttcgaacttaacataatttgcttctctggggatgaaattctgatattgtgtttgttgttgggtcaattttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACAATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCAGTTTCAAAAGATTC

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|32930091|gb|CF034903.1|CF034903
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|67019503|gb|CO448252.1|CO448252
EST:     GCATATGCTGGGCCAAAT-GTTGCTGTTTTTGGTGGTGATTGTGCATCAG                         GCGATACATTTACGGATGGGACAGTGAAATATACTATGACTTCAATGAATG
genomic: GCATATGCTGG-CCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|91874831|gb|EB404788.1|EB404788
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|211410070|gb|FL355701.1|FL355701
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTT-AATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|118406757|gb|EH038205.1|EH038205
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|211409847|gb|FL347405.1|FL347405
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|67017174|gb|CO445923.1|CO445923
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|211430479|gb|FL350077.1|FL350077
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG

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: 143

GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 146

GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 195

GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgtttacttcatttattctggatctgacttttcacttctctttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC
                         atctgac  putative branch site (score: 195)
                          tctgacttttcacttc  CT-rich tract
      tttacttcatttatt  TA-rich tract