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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatctgagccccccttcactcctgaattttaattcaaactgtcatatctcgttctgcgactttcttttgctcgatggaagcattagtttgtagtc...

Basic information

species Zea mays
transcript GRMZM2G119773_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119773_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g56970.2 (Oryza sativa), 5'ss of exon 3
TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatctgagccccccttcactcctgaattttaattcaaactgtcatatctcgttctgcgactttcttttgctcgatggaagcattagtttgtagtc--
||||||||||||||| ||||||||||||||||| |||||||| || ||||| ||||| ||||||||||||||||| || || || ||||||||| | ||||||||| | |||| |  | | ||| | |  |   | | |    | || | || |  |     |  ||  ||  ||  |    || ||||   ||   |    
TGCTCCAGTTGTTGCTCAGATATCAAAGGAAGCCGGTTATCTCACCGTTGGAGTTGTTACCTATCCATTCAGTTTTGAAGGACGCAAGCGCTCTCTTCAGgcaagtgtttgagtcttc-tccacccgtatacaattaatgtggc-gttacatttgataaatagttttggttaagcatggaacaaacatttccttaggggagc

upper sequence: GRMZM2G119773_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g56970.1 (Oryza sativa), 5'ss of exon 3
TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatctgagccccccttcactcctgaattttaattcaaactgtcatatctcgttctgcgactttcttttgctcgatggaagcattagtttgtagtc--------
      ||||||||| ||||||||||||||||| |||||||| || ||||| ||||| ||||||||||||||||| || || || ||||||||| | ||||||||| | |||| |  | | ||| | |  |   | | |    | || | || |  |     |  ||  ||  ||  |    || ||||   ||   |          
------AGTTGTTGCTCAGATATCAAAGGAAGCCGGTTATCTCACCGTTGGAGTTGTTACCTATCCATTCAGTTTTGAAGGACGCAAGCGCTCTCTTCAGGCAAGTgtttgagtcttc-tccacccgtatacaattaatgtggc-gttacatttgataaatagttttggttaagcatggaacaaacatttccttaggggagctgtgag

upper sequence: GRMZM2G119773_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaa-gtatctgagccccccttcactcctgaattttaattcaaactgtcatatctcgttctgcgactttcttttgctcgatggaagcat-tagtttgtagtc
||| || || || || ||||| || ||||| ||||||||| | |||||||||||||| |||||||| || || || || || |||||  | ||| | |||| || || | |   | ||  |||  |  |||||     || ||  | | |  ||| ||| ||   || |   |   | | |     | | |||         
TGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaatgtgtgttgacaccgtttc-ttgttgaat--gggtttaagtt-taaagtcttgttatggatctatgcctgatttggttatttcctctag---------

upper sequence: GRMZM2G119773_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 5'ss of exon 3
TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatctgagccccccttcactcctgaattttaattcaaactgtcatatctcgttctgcgactt-tcttttgctcgatggaagcattagtttgtagtc-------
||| |||||||||||||| ||||| |||||||| |||||| | |||||||| || |||||||| || ||||| || || || |||||  | ||  | |||||| ||         ||  ||   || | | ||  |||  ||       ||| | ||| |  | ||  ||||    |  ||| ||  ||||  ||  |          
TGCCCCAGTTGTTGCCCAAATATCTAAGGAAGCGGGTTATTTGACTGTTGGGGTGGTCACCTACCCTTTCAGCTTTGAAGGACGTAAAAGATCACTGCAGgcaggtg--------ccattttggtctttatttgaaatcaaagggaaattattttgttgtttgtctggtcttactatatatgtaacaattaacttccaaatgacaggc

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|148970650|gb|EE021357.2|EE021357
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|149107184|gb|EE189070.2|EE189070
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|20508091|gb|BQ279894.1|BQ279894
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|211173948|gb|FL234238.1|FL234238
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|148940468|gb|EC885267.2|EC885267
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|211174836|gb|FL413961.1|FL413961
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|31998233|gb|CD661991.1|CD661991
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAA
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAA
EST: gi|76923027|gb|DV169298.1|DV169298
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|148941071|gb|EC885931.2|EC885931
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|149097959|gb|EE183902.2|EE183902
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|149097351|gb|EE183189.2|EE183189
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|88755311|gb|DY539452.1|DY539452
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|74235120|gb|DT643034.1|DT643034
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|211175625|gb|FL234251.1|FL234251
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|60356845|gb|DN223818.1|DN223818
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|78078489|gb|DV506902.1|DV506902
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|149013929|gb|EE043427.2|EE043427
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|20507237|gb|BQ279544.1|BQ279544
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGA
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGA
EST: gi|71450106|gb|DR831156.1|DR831156
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|148964386|gb|EC905762.2|EC905762
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|71305508|gb|DR788897.1|DR788897
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|148942194|gb|EC887199.2|EC887199
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|211478791|gb|FL377823.1|FL377823
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|71431993|gb|DR813043.1|DR813043
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
EST: gi|148971012|gb|EE021841.2|EE021841
EST:     GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAG                         GCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG
genomic: GTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTG

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: 278

TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTGATTCCAAATGATAAGTTATTAGATGTTGCGGATGAAAACATGCCCTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTGATTCCAAATGATAAGTTATTAGATGTTGCGGATGAAAACATGCCCTTGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 73

TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTGATTCCAAATGATAAGTTATTAGATGTTGCGGATGAAAACATGCCCTTGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 135

TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatct ... cccattttagGCATTGGAAGCACTAGAGAAGCTGGAAAAGAGTGTAGACACACTTATTGTGATTCCAAATGATAAGTTATTAGATGTTGCGGATGAAAACATGCCCTTGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaagtatctgagccccccttcactcctgaattttaattcaaactgtcatatctcgttctgcgactttcttttgctcgatggaagcattagtttgtagtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccct