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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctattcgtttaacgtagttttgttgcttttcaagtttctggatatatagaatatatattttactcattttaatcctactttatttcacaatttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT

Basic information

species Zea mays
transcript GRMZM2G121790_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 6
cctattcgtttaacgtagttttgttgcttttcaagtttctg--gatatatagaatatatattttactcattttaatcctactttatttcacaatt--tgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT
   ||     | || | | | | || |||||    ||| |   | | ||  | |  | || | | |||||||| ||| | ||||      ||||   ||  ||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||| || |||||||||||||| || ||||| |||||||||||||| |
---atcaacctcacattgctgtatttcttttttcttttatattgctgtaatgcaactctactgtcctcattttgatc-tgcttttccattcaatcgctgggcagGTTAAAGGTGAAGCAAACATATCGTATATATGTTCACGTTATTACCGTGCTCCAGAACTGATATTTGGGGCAACCGAATACACGACATCAATTGATATAT

upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
-----cctattcgtttaacgtagttttgttgcttttcaagtttctggatatatagaatatatattttactcattttaatcctactttatttcacaatttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT
        | | |||   | || | | |    || ||  ||       |   | ||||   |   |    ||||   ||| || |    ||    | |||  ||||| ||||| ||  | || || || || || |||||||| |||||||||||||| ||||| |||||||| || || || ||||||||  | ||||| || |
gagtctgcagtggttgctcataatatgga-aattgtctcgtgcggtattcagttgaatgcgtgggtgcagcatt--gatcatagtgagatttg--agttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT

upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 5
cctattcgttta-acgtagttttgttgcttttcaagtttctggatatatagaatatatattttactcattttaatcctactttatttcacaatttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT
  || | | | | || | |  |   |  | |        ||       | |||||| |   |     |  |     |      | |||      ||  ||||| ||||| ||| | ||||| || ||||| |||||||| |||||||||||||| ||||| |||||||| || || || ||||| ||  | || || || |
agtagtgggtaacacatggcatgaataatgtcttctccgctat-cgagttgaatatttgagtggagaaagtggcgacactgagaattcgagtactgtgcagGTGAAAGGGGAACCTAACATCTCGTATATCTGTTCACGGTATTACCGTGCTCCTGAGCTGATATTTGGAGCGACGGAATACACCACTGCGATAGACATAT

upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 7
cctattcgtttaacgtagttttgttgcttttcaagtttctggatatatagaatata-tattttactcattttaatcctactttatttcacaatttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT
                    | | |||||   ||      ||||   | ||||  |  |  | | |    ||  |||| ||||  ||  |||    | ||||| ||||| ||  | |||||||| ||||| ||||| ||||||||||||||||| || || |||||||| |||||||| ||||||||| | || || || |
-------------------gtgggtgcttacaaa----taggatccttggaattcagcagctgatttgcgtt--tcctgcttttcttggcaaaacaaacagGTGAAAGGAGAGCCCAACATATCGTATATCTGTTCCCGTTATTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 7
cctattcgtttaacgtagttttgttgcttttcaagtttctggatatatagaatata-tattttactcattttaatcctactttatttcacaatttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT
                    | | |||||   ||      ||||   | ||||  |  |  | | |    ||  |||| ||||   |  |||    | ||||| || || ||  | |||||||| ||||| ||||| ||||| ||||||||||| || || |||||||| |||||||| ||||||||| | || || || |
-------------------gtgggtgcttacaaa----taggatccttggaattcagcagctgatttgcgtt--tcctgcttttcctggcaaaacaa-cagGTGAAGGGAGAGCCCAACATATCGTATATCTGTTCCCGTTACTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

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|19770441|gb|BQ035162.1|BQ035162
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|148952787|gb|EC898773.2|EC898773
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAGAGGTGAAGCAAACATATCATATATATGTTCA
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCA
EST: gi|148932530|gb|EC876330.2|EC876330
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|76287882|gb|DV027450.1|DV027450
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATG
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATG
EST: gi|211251114|gb|FL353291.1|FL353291
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|71441697|gb|DR822747.1|DR822747
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|32855414|gb|CD995095.1|CD995095
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAGGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|211298028|gb|FL233897.1|FL233897
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|33098911|gb|CF058871.1|CF058871
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|94476799|gb|EB705757.1|EB705757
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAAGCAA-CATATCATATATATGTTCACGTTAT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAA-GCAAACATATCATATATATGTTCACGTTAT
EST: gi|149112787|gb|EE191425.2|EE191425
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|71430638|gb|DR811688.1|DR811688
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|211326797|gb|FL341548.1|FL341548
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|31351371|gb|CD435728.1|CD435728
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|71443964|gb|DR825014.1|DR825014
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGT
EST: gi|211298026|gb|FL233895.1|FL233895
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTRCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|148931707|gb|EC874917.2|EC874917
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAAGCAA-CATATCATATATATGTT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAA-GCAAACATATCATATATATGTT
EST: gi|76922778|gb|DV169169.1|DV169169
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCNAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
EST: gi|20300401|gb|BQ163344.1|BQ163344
EST:     CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG                         GTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT
genomic: CACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCT

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: 272

GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTGgtaagttaat ... atttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagaatatatattttactcattttaatcctactttatttcacaatttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT
                      ttttaat  putative branch site (score: 183)
     aatatatattttactc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctattcgtttaacgtagttttgttgcttttcaagtttctggatatatagaatatatattttactcattttaatcctactttatttcacaatttgatcagGTCAAAGGTGAAGCAAACATATCATATATATGTTCACGTTATTACCGTGCTCCAGAGCTCATATTTGGGGCAACTGAGTACACAACATCAATTGATATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - -tgttgct