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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgttgtcaaatttatattataaccataagtttgactcccgcttacggggctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT

Basic information

species Zea mays
transcript GRMZM2G126361_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 2
gtaaatgttgtca--aatttatattataaccataagtttgactcccgcttacggggctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
|||||| ||||||  |  |||  || | ||  | || |  | |    ||   | | |  ||||||||||||  || |||||||||  |||||| ||||||||| ||||||||||| || ||||||||||| || ||||| || || || |||||||||||||| |||||||| || ||||||||||||||||||||
gtaaatcttgtcaccatattaacttgtgact-tgagctgaaattatcctggtgtg-cagaggttcctaatccatttttgaacttttcaatttgcagAGGCTGGTCATGCCCTTGTTGGTGCCCTCATGCCTGAATATGACCCTGTTGCTAAGATTTCCATCATTCCTCGTGGTCAAGCTGGTGGACTCACATTCTT

upper sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 2
gtaaatgttgtcaaatttatattataaccataagtttgactcccgcttacggg-gctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
|||    || |    || || ||  |  |  |||||||      | |    ||   |  |||    || || || ||   | |    ||||  ||||||||||||||| || || || ||  | ||||| || ||||| || ||||||||||| || || || ||||||||||| |||||||| |||||||| ||
gtatgcattttttttttaatgttcaacacgcaagtttgttaagagttggttggtatttgggtattcaaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT

upper sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 2
gtaaatgttgt-caaatttatattataaccataagtttgactcccgcttacggggctc-aggttcctaatctgttgttgaactttgg-aatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
         ||    |||| | |||| |||  |||||||      | |     |  |   |||    || || || ||   || ||   ||||  ||||||||||||||| || || || ||  | |||||||| ||||| || ||||||||||| || || || ||||||||||| |||||||| |||||||| ||
---------gtatgcattttttttattacc-caagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT

upper sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaatgttgtcaaatttatatta-taaccataagtttgactcccgcttacggggctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
               |  ||| || | | | ||  |    ||   | |      |    |    || | |||||    ||  ||| |||||| ||||||||| |||||  | || || || || ||||| |||||||||||||| |||||||| || || || || |||||||| |||||||| ||||| || ||
-------------gttagatactactgatcctagctacttcttgtgttattattgtgttgaccactca-ctgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT

upper sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaatgttgtcaaatttatattataaccataagtt-tgactcccgcttacggggctcaggttc-ctaatctgtt--gttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
         || |   || |||  |||| ||| ||  ||     |||    |||  ||  |||  || | |   |    |||| |||  |||||  ||||||||| ||||| || || || || || |||||||| |||||||| || || |||||||| ||||| ||||||||||| |||||||| ||||| || ||
---------gttagcattttatc-taactatatgtaatggagtacgcagctgggattcttgttttctgaccacctcaaatgaatttta-aatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT

upper sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ31931 (Selaginella moellendorffii), 3'ss of exon 2
gtaaatgttgtcaaatttatattataaccataagtttgactcccgcttacggggctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
                        ||| || || | | ||||    || ||    || ||| | |||   |         ||||     |||||||||||||||||| || || || || || ||||| ||||||||||| || || || |||||||||||||| || ||    || || ||  | || || ||
-----------------------gtaagca-aactctcactcttagtttcg----tcgggtacttaactcg-----agtttttgttgaatgtagAGGCTGGCCATGCACTCGTTGGAGCACTGATGCCCGAGTATGATCCCGTCGCGAAAATTTCCATCATCCCCCGCGGTGGAGCCGGAGGTTTGACCTTTTT

upper sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ37923 (Selaginella moellendorffii), 3'ss of exon 2
gtaaatgttgtcaaatttatattataaccataagtttgactcccgcttacggggctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
                        ||| || || | | |||     || ||    || ||  | || ||   | ||     |||||    |||||||||||||| || || || || || || ||||| |||||||||||||| || || |||||||||||||| || ||    || || ||  | ||||| ||
-----------------------gtaagca-aactctcacttttagtttcg----tcggggacttactcgagtttttg---ttgga----gtagAGGCTGGCCACGCACTCGTTGGAGCACTGATGCCCGAGTATGATCCAGTCGCGAAAATTTCCATCATCCCCCGGGGTGGAGCCGGAGGTTTGACATTTTT

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|93283832|gb|EB676096.1|EB676096
EST:     GAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATG                         AGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAA
genomic: GAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
EST: gi|13198172|gb|BG354188.1|BG354188
EST:     CCGAGGAGAAGAAGAGGCTCGTCGCTTACCATG                         AGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
genomic: CCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
EST: gi|13149600|gb|BG319922.1|BG319922
EST:     GAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATG                         AGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
genomic: GAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
EST: gi|211089719|gb|FL375369.1|FL375369
EST:     AAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATG                         AGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
genomic: AAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
EST: gi|33092826|gb|CF052820.1|CF052820
EST:     GAAAAATGCTGTTGTTTTCGAGGAGAAGAAGAGGCTCGTCGCTTACCATG                         AGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
genomic: GAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
EST: gi|32916795|gb|CF021607.1|CF021607
EST:     GAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATG                         AGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
genomic: GAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
EST: gi|32828250|gb|CD967928.1|CD967928
EST:     GAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATG                         AGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
genomic: GAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
EST: gi|71761686|gb|DR959623.1|DR959623
EST:     AGGAGAAGAAGAGGCTCGTCGCTTACCATG                         AGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG
genomic: AGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAG

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: 92

AAGGATGAGATCTCTGATGCTCTTGAGAGAATCATTGCTGGCCCTGAGAAGAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 356

AAGGATGAGATCTCTGATGCTCTTGAGAGAATCATTGCTGGCCCTGAGAAGAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

AAGGATGAGATCTCTGATGCTCTTGAGAGAATCATTGCTGGCCCTGAGAAGAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 369

AAGGATGAGATCTCTGATGCTCTTGAGAGAATCATTGCTGGCCCTGAGAAGAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgtaaatgttg ... gaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcccgcttacggggctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
                      tcctaat  putative branch site (score: 369)
                                              aatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgttgtcaaatttatattataaccataagtttgactcccgcttacggggctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA