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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccttttctcgttgctatagactatagtatgaattttgttctaaacacagatataatattcagataatactcatctctgaaggatatctaccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT

Basic information

species Zea mays
transcript GRMZM2G066440_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066440_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 6
gccttttctcgttgctatagactatagtatgaattttgttctaaacacagatataatattcagataatactcatctctg--aaggatatctaccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT
  | ||| || ||  || |     |  | |    ||     ||  ||||  | |   ||||| ||   |||||  ||||  | |||        || |  |||| | |||||| |||||||||||||||||||||||||||||||| ||||||||||||||| | | |  | | ||||| ||||||||||| ||||||||||
ctcctttttcattagtacatttactgatttaggcttatggtta--cacatctgtcggattcacatttcactcaattctgtcatggactgtgtgtttctgtagGTACAGCAAGCGGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGGCCAATTGCTCTTAGGAATCGTGATATTGTAGCTGTGGCGAAGACAGGTT

upper sequence: GRMZM2G066440_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G14610.1 (Arabidopsis thaliana), 3'ss of exon 6
--gccttttctcgttgctatagactatagtatgaattttgttctaaacacagatataatattcagataatactcatctctgaaggatatctaccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT
  || | |||| | | | |||  | | |||| || ||||| | |              |  || | | | |   || ||     | | | |   ||| ||||||       ||||||||||| || ||| |||| || ||||||||||||||||||||||| ||| |    || || ||||||||  | || || ||||| |
gtgcttcttctggct-ccataagc-acagta-gatttttggtgt--------------ttctctgctgaaaaggatatcc---tggtttgttgttttgccagGTATACAGTGCAGGATTCTCAGCTCCATCTCCAATTCAAGCTCAGTCATGGCCAATTGCGATGCAAAACAGAGACATAGTAGCCATTGCTAAAACAGGCT

upper sequence: GRMZM2G066440_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G14610.2 (Arabidopsis thaliana), 3'ss of exon 4
gccttttctcgttgctatagactatagtatgaattttgttctaaa--cacagatataata---ttcagataatactcatctctgaaggatatc--------taccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT
              ||  | ||   || |||    || ||||     || |   | | ||   ||  | |  | |||  ||   |||||||||        |   ||| ||||||       ||||||||||| || ||| |||| || ||||||||||||||||||||||| ||| |    || || ||||||||  | || || ||||| |
-------------cctgcaaacgggaggatggtgcttcttctggctccataagcacagtagatttttggtgtttctctgctgaaaaggatatcctggtttgttgttttgccagGTATACAGTGCAGGATTCTCAGCTCCATCTCCAATTCAAGCTCAGTCATGGCCAATTGCGATGCAAAACAGAGACATAGTAGCCATTGCTAAAACAGGCT

upper sequence: GRMZM2G066440_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 4
gccttttctcgttgctatagactatagtatgaatt-ttgttctaaacacagatataatattcagataatactcatctctgaag-------gatatctaccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT
          | || |      | |   ||||       ||| | |  |  | |  | |    | |  | | | ||||  | |       | | |     |||   |||| ||    ||||| |||||||| |||||||| || ||||||||||||||||| ||||||||| | |||||||| ||||||||  | || || || || |
-------ggggatggtgcttcttctgacatgagccaccattccataagcccaaaaga-accttggtgttccccttctcataggacagtgtggttttctgttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGGCCCATTGCTATGCAAGGTAGGGACATAGTAGCCATTGCTAAAACTGGCT

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|211413817|gb|FL421626.1|FL421626
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211271873|gb|FL420608.1|FL420608
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211453719|gb|FL371690.1|FL371690
EST:     ATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATG
genomic: ATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTC-TAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATG
EST: gi|211479925|gb|FL425093.1|FL425093
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211271148|gb|FL388759.1|FL388759
EST:     ATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATG
genomic: ATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGG-AGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATG
EST: gi|211089720|gb|FL375370.1|FL375370
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211273933|gb|FL428371.1|FL428371
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGNCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211059644|gb|FL374516.1|FL374516
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|78120608|gb|DV538992.1|DV538992
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATTCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211233915|gb|FL394219.1|FL394219
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211210029|gb|FL411366.1|FL411366
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211218085|gb|FL424499.1|FL424499
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211485264|gb|FL406762.1|FL406762
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|78122609|gb|DV540993.1|DV540993
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAGGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCATCTCCTATCCAAGCTCAGTCGTGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211450321|gb|FL410319.1|FL410319
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211158229|gb|FL401285.1|FL401285
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211339029|gb|FL403594.1|FL403594
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211204746|gb|FL408304.1|FL408304
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211282425|gb|FL393384.1|FL393384
EST:     ATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: ATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATT-CTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211229498|gb|FL371568.1|FL371568
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211179793|gb|FL384665.1|FL384665
EST:     ATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: ATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATT-CTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211527411|gb|FL405481.1|FL405481
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211487815|gb|FL394402.1|FL394402
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|149072975|gb|EE161236.2|EE161236
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCCACTCCTATCCCAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211374582|gb|FL413733.1|FL413733
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
EST: gi|211521604|gb|FL412478.1|FL412478
EST:     CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG                         GTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG
genomic: CATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 161

GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 80

GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 101

GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAGgtaagtctac ... ccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacagatataatattcagataatactcatctctgaaggatatctaccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT
                                       tatctaccttttcc  CT-rich tract
     atataatattcagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccttttctcgttgctatagactatagtatgaattttgttctaaacacagatataatattcagataatactcatctctgaaggatatctaccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - -cgttgct
- - - - - - - - - - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - - - - - - - aaacaca