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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttactaagactctgcattggagtactggattaatcttgaccatatctgtcgcaactctgtggtgcttgtcttgataagtctctcttgcaattttttttgttttttcatgataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA

Basic information

species Zea mays
transcript GRMZM2G386991_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g62080.2 (Oryza sativa), 3'ss of exon 11
gttagtttactaagactctgcattggagtactggattaatcttgaccatatctgtcgcaactctgtggtgcttgtcttgataagtctctcttgcaattttttttgttttttcatgataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA
||||||| ||  |   |||  |   ||||| |   || || ||  | ||| |     ||   | | | | |  |  ||   |   ||  ||    || | ||   | |||   |     || ||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||  ||  |||| || || ||||| ||||||||||||||||||||
gttagttcac--actatctatacctgagtagttccttgattttctctatagcc----cagtgccg-gctccgcgaatttgcagtgcttcctattgatatgttgcctctttgattttctctactagGGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G53570.2 (Arabidopsis thaliana), 3'ss of exon 10
gttagtttactaagactctgcattggagtactggattaatcttgaccatatctgtcgcaactctgtggtgcttgtcttgataagtctctcttgcaattttttttgttttttcatgataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA
                             | |   || || ||  | ||||||  ||  || |     |  |  |||    | |||||  |     |||| | ||  ||      |   |   |||| || || || || ||||| |||||||||||||| |||||||| |||||||| | |||| |||| ||| | |||   |||||| |  ||||||| ||
--------------------------gtgagtaactttatgtttgc-atatcttccggtacaccaccctattcatctcaccatgtctccatcaacgttttctctggatt-----aaaccttgcagGGAGAGGCGCTTTTCCAAACGCATGAAAACTTGGAACATTTGGCCATGATGGAAAGGGTCCTAGGACCTTTACCACCTCATATGGTGCTCAGAGCCGA

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 11
gttagtttactaagactctgcattggagtactggattaatcttgaccatatctgtcgcaactctgtggtgcttgtcttgataagtctctcttgcaattttttttgttttttcatgataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA
               |   | |   |  ||||| |    | |  || | |  || ||  |  |    || | ||  |  ||| |||| | |   || ||| ||  || |||        | |||||| || || || ||||| || ||||| |||||||||||||||||||||||||||  ||| ||||| ||  | ||    || |||||    || || ||
-------------tccctcgaagaaggctactgtagctgtatctactacacatgacggtagcc----gtacatggatcaatatgtct-tttaataactttattcattgttt-------gttttagGGTGATGCGCTGTTTCAGACTCATGAGAACTTGGAGCATTTGGCTATGATGGAGCGGGTTTTAGGTCCCATTCCCGTTCACATGATAAGGAGGGCAGA

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|211512137|gb|FL430403.1|FL430403
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACAC
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACAC
EST: gi|6021499|gb|AW066427.1|AW066427
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|211073306|gb|FL473576.1|FL473576
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|19822133|gb|BQ048157.1|BQ048157
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|19769731|gb|BQ034452.1|BQ034452
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|19769965|gb|BQ034686.1|BQ034686
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|31997648|gb|CD661693.1|CD661693
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|211122243|gb|FL474055.1|FL474055
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|211212596|gb|FL411382.1|FL411382
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|19822056|gb|BQ048080.1|BQ048080
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|15426933|gb|BI542755.1|BI542755
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|15352988|gb|BI502599.1|BI502599
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|14245195|gb|BG873777.1|BG873777
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|60343108|gb|DN210081.1|DN210081
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|60354602|gb|DN221575.1|DN221575
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|45847998|gb|CN071941.1|CN071941
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACCTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
EST: gi|6127284|gb|AW129809.1|AW129809
EST:     ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG                         GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG
genomic: ATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATG

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), 45 (downstream exon)
Score: 194

GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 304

GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 236

GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCGgttagtttac ... ataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtcttgataagtctctcttgcaattttttttgttttttcatgataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA
    tcttgat  putative branch site (score: 236)
                    ttgcaattttttttgt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttactaagactctgcattggagtactggattaatcttgaccatatctgtcgcaactctgtggtgcttgtcttgataagtctctcttgcaattttttttgttttttcatgataatattagGGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGA

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