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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtacaagtcttttgttatcttcttatcatactttttgtcatttttatttatgtatacatccaagatgaggtatctgatcagttctgttttcgcttatcttattaacctatttattaatgctgtttttacag

Basic information

species Zea mays
transcript GRMZM2G386991_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g62080.2 (Oryza sativa), 5'ss of exon 12
GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtacaagtcttttgttatcttcttatcatactttttgtcatttttattta---tgtatacatccaagatgaggtatctgatcagttctgttt-----tcgcttatcttattaacc---------tatttattaatgctgtttttacag
|| |||||||||||||||||||||||||| |||||||||||||||||||||||||  ||  |||| || || ||||| |||||||||||||||||||||||||| ||||||   || |||||  | | || ||  || || | || |    | |    || |||||| | | | ||||  ||| | ||||   | |     ||  | |  |||| || |         || || ||| | || |||||||||
GGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatacaaggtcttcgttatagtttcatgat--ttattataatctaagataagatggtttacatctaggcttaggttgctgctgagtttcatctgaagttctttcaaattatcaatcacttgcatgtacttgttacttct-tttttacag

upper sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT3G53570.2 (Arabidopsis thaliana), 5'ss of exon 11
GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtacaagtcttttgttatcttct-tatcatactttttgtcatttttatttatgtatacatccaagatgaggtatctgatcagttctgttttcgcttatcttattaacctatttattaatgctgtttttacag
|| || || || || ||||| |||||||||||||| |||||||| |||||||| | |||| |||| ||| | |||   |||||| |  ||||||| ||||| |   |  | | |  |  ||| | |   |||| |         |   | | ||       |||     ||     |    | ||   | ||| | ||                                      
GGAGAGGCGCTTTTCCAAACGCATGAAAACTTGGAACATTTGGCCATGATGGAAAGGGTCCTAGGACCTTTACCACCTCATATGGTGCTCAGAGCCGAgtaagaacaataatatcatcctatttgcagcatcagataccagcagaaaataacttgaactgtcatttcttatatcaaa----accaaaacggttcttgcag------------------------------------

upper sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 5'ss of exon 12
GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtacaagtcttttgttatcttcttatcatactt--tttgtcatttttatttatgtatacatccaagatgaggtatc-tgatcagttctgttttcgctt----atcttattaacctatttattaatgctgtttttacag------------------------------------
|| || || || ||||| || ||||| |||||||||||||||||||||||||||  ||| ||||| ||  | ||    || |||||    || || ||||| || |       | ||    |  | ||  |  | ||  |||| |  |  | |   | ||   |        |||   ||  | | ||||||||       |     | |||   ||   |  ||   |   |  ||||                                       
GGTGATGCGCTGTTTCAGACTCATGAGAACTTGGAGCATTTGGCTATGATGGAGCGGGTTTTAGGTCCCATTCCCGTTCACATGATAAGGAGGGCAGAgtacgttttttttcttgttaactttattttgcccaaattactttggctatcctgtcggtttacttaatggtatagagtggtcacgctgagttctgtgcgtatgttaaggttttaccgactagtaaatgtctatggactttaatattgctaacatgttgtatggattacacaaatattcag

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|211421941|gb|FL433263.1|FL433263
EST:     TGGAGAAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: TGGAG-AAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|113702476|gb|EE679980.1|EE679980
EST:     AGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: AGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|6021499|gb|AW066427.1|AW066427
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|211073306|gb|FL473576.1|FL473576
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGTGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|19822133|gb|BQ048157.1|BQ048157
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|19769731|gb|BQ034452.1|BQ034452
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|19769965|gb|BQ034686.1|BQ034686
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|19769330|gb|BQ034051.1|BQ034051
EST:     AGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: AGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|31997648|gb|CD661693.1|CD661693
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|211122243|gb|FL474055.1|FL474055
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGTGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|211212596|gb|FL411382.1|FL411382
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAWAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAG
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAG
EST: gi|19822056|gb|BQ048080.1|BQ048080
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|15426933|gb|BI542755.1|BI542755
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|15352988|gb|BI502599.1|BI502599
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|14245195|gb|BG873777.1|BG873777
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|60343108|gb|DN210081.1|DN210081
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|60354602|gb|DN221575.1|DN221575
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|45847998|gb|CN071941.1|CN071941
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
EST: gi|6127284|gb|AW129809.1|AW129809
EST:     ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA                         TCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGA

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: 134

GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 153

GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 116

GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtac ... gtttttacagTCGGCGTGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtacaagtcttttgttatcttcttatcatactttttgtcatttttatttatgtatacatccaagatgaggtatctgatcagttctgttttcgcttatcttattaacctatttattaatgctgtttttacag

- - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA