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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGATGATGTCGTAGTTCCCTGCGGCAAGCCGGTGCCATCATCAATTAGGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagtgttctttttaccctatctatccctttgcttttccagtgctgcgggttcataggggatgtgcacactgaccttttgtgaaaacctgtgtgtgtgtgccatcag

Basic information

species Zea mays
transcript GRMZM5G831712_T02
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G831712_T02 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os07g23110.1 (Oryza sativa), 5'ss of exon 19
GAGGGATGATGTCGTAGTTCCCTGCGGCAAGCCGGTGCCATCATCAATTAGGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagtgttctttttaccctatctatccctttgcttttccagtgctgcgggttcataggggatgtgcacactgaccttttgtgaaaacctgtgtgtgtgtgccatcag
|||||||||||| || || || ||||| ||||| |||||| |||| || | ||  ||||| || |||||||||||||| || |||||||| ||||||||||||||   ||    || ||| ||    ||  | |||||       | ||| | | |||||  |   |       || ||||||   |||| | | | | ||   |       
GAGGGATGATGTTGTGGTGCCATGCGGAAAGCCAGTGCCAGCATCTATCAAGACATCTGAGCTTATGTACAATGAGTATATTGTCTACAATACATCCCAGgttca---gtcaaattgttatcca---tactcttttgc-------gcgcttctg-ttcatcagaagttcagttccttacctttcacgaaaccttatctctggcag-------
















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|8516713|gb|BE123437.1|BE123437
EST:     GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAG                         GTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
genomic: GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
EST: gi|61119038|gb|DN559999.1|DN559999
EST:     GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAG                         GTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
genomic: GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
EST: gi|60351643|gb|DN218616.1|DN218616
EST:     GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAG                         GTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
genomic: GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
EST: gi|60394841|gb|DN227710.1|DN227710
EST:     GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAG                         GTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
genomic: GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
EST: gi|211088585|gb|FL093444.1|FL093444
EST:     GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAG                         GTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
genomic: GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
EST: gi|8516247|gb|BE122975.1|BE122975
EST:     GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAG                         GTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
genomic: GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
EST: gi|9028469|gb|BE238464.1|BE238464
EST:     GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAG                         GTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
genomic: GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
EST: gi|60350335|gb|DN217308.1|DN217308
EST:     GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAG                         GTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
genomic: GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
EST: gi|94475979|gb|EB704937.1|EB704937
EST:     GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAG                         GTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG
genomic: GGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTG

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: 116

GAGGGATGATGTCGTAGTTCCCTGCGGCAAGCCGGTGCCATCATCAATTAGGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTGGGAGACTAGGCAAGTAGAGTTGGAAGGTAGAGAAGCAGAGTTAGGCGAT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 29

GAGGGATGATGTCGTAGTTCCCTGCGGCAAGCCGGTGCCATCATCAATTAGGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTGGGAGACTAGGCAAGTAGAGTTGGAAGGTAGAGAAGCAGAGTTAGGCGAT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 27

GAGGGATGATGTCGTAGTTCCCTGCGGCAAGCCGGTGCCATCATCAATTAGGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTGGGAGACTAGGCAAGTAGAGTTGGAAGGTAGAGAAGCAGAGTTAGGCGAT


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 30

GAGGGATGATGTCGTAGTTCCCTGCGGCAAGCCGGTGCCATCATCAATTAGGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagt ... gtgccatcagGTGAAGATGCAGTTCTTGCTGAAGGTGCGTTTCCATCACAAGAGGTAGCTGGGAGACTAGGCAAGTAGAGTTGGAAGGTAGAGAAGCAGAGTTAGGCGAT


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGATGATGTCGTAGTTCCCTGCGGCAAGCCGGTGCCATCATCAATTAGGAGCTCTGAACTCATGTACAATGAGTACATCGTCTACAACACATCCCAGgttcacaagtgttctttttaccctatctatccctttgcttttccagtgctgcgggttcataggggatgtgcacactgaccttttgtgaaaacctgtgtgtgtgtgccatcag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT