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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgtagagccataacaaaccatgaaccatcagatgtactgccagtgcagtgtggaatgaacctagcctggaaactcatataacggagtttgaaatctttctatcattctattcatgtttgctcataggaccattcgtctaatgtcgctcagcacacccattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACACTGGTCCAGACTTTTGGGCAGAAGGATCATGTCTGCCTGAAGGAAGGCT

Basic information

species Zea mays
transcript GRMZM2G056702_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 2
gtgagttgtagagccataacaaaccatgaaccatcagatgtactgccagtgcagtgtggaatgaacctagcctggaaactca-tataacggagt--ttgaaatctt-tctatcattctattcatgtttgctcataggaccattcg-tctaatgt-cgctcagcacacccattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACACTGGTCCAGACTTTTGGGCAGAAGGATCATGTCTGCCTGAAGGAAGGCT
|| | |    ||  ||| |   ||| ||||| ||   || |     ||  | |   |   |||| |||   ||  | ||||| || |||| | |  || |  ||   | || || |   | |   ||| |   |   |||||  | ||| || | |  |  |     ||||  ||||||||||||||||||| ||||||||  |||| || |||||||||||||| || |||||||||||||||||||||||||||||||||||||| |||||||| |
gtaaatcaaggaatcatta---accttgaactattgtatatcaaatcatggaaacatacgatgagcctcatctacatactcaatacaacgaaatcattcagctccaatgtaccaattgttacccttttacatgttcaaccatgggatcttatttgcatttggtttttccatgattcagGAAGAGAAGGCCATTGAGCGGGGAATCCTGCCATTGCTTCGCCGTGCGACGCTGGTCCAGACTTTTGGGCAGAAGGATCATGTCTGCCTCAAGGAAGGGT
















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|50322792|gb|CO517918.1|CO517918
EST:     CCACTTCCCCTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: CCACTT-CTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|67029426|gb|CO458175.1|CO458175
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|148962163|gb|EE012976.2|EE012976
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|29947042|gb|CB816453.1|CB816453
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|71445976|gb|DR827026.1|DR827026
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|149090404|gb|EE179713.2|EE179713
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|148955685|gb|EC901365.2|EC901365
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|149013255|gb|EE042858.2|EE042858
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|149043975|gb|EE047456.2|EE047456
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|148951471|gb|EC897197.2|EC897197
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|149008403|gb|EE040559.2|EE040559
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|148947061|gb|EC892363.2|EC892363
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|71430156|gb|DR811206.1|DR811206
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|91048368|gb|EB158786.1|EB158786
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|76284997|gb|DV024565.1|DV024565
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|148964683|gb|EC905962.2|EC905962
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|71444106|gb|DR825156.1|DR825156
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAACGAGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|71767069|gb|DR965006.1|DR965006
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|149071087|gb|EE159488.2|EE159488
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|71442524|gb|DR823574.1|DR823574
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|148962339|gb|EE013175.2|EE013175
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|71764094|gb|DR962031.1|DR962031
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|31909763|gb|CD651082.1|CD651082
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|149109269|gb|EE190110.2|EE190110
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAAGAAGGCCATCGAGCGGGG
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGA-GAAGGCCATCGAGCGGGG
EST: gi|149000409|gb|EE037579.2|EE037579
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCCTTCCGTTGCTTCGCCGTGCTAC
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCC-TTCCGTTGCTTCGCCGTGCTAC
EST: gi|148967632|gb|EE018888.2|EE018888
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|148952079|gb|EC897870.2|EC897870
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|91877857|gb|EB407814.1|EB407814
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCCTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|149070619|gb|EE159030.2|EE159030
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCCGT-GCTTCCCCGTGCTAC
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCC-GTTGCTTCGCCGTGCTAC
EST: gi|148936286|gb|EC880367.2|EC880367
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|76020818|gb|DT947988.1|DT947988
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|148956918|gb|EC902847.2|EC902847
EST:     ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
genomic: ACCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACCAGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACA
EST: gi|148930698|gb|EC872947.2|EC872947
EST:     CCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCCCTACCCAG                         GAAGAGAAGGCCATCGAGCGGGGCGTCCTTCC
genomic: CCACTTCTTTGTCGTGCCACATGACTTTGGCGCATGCTTCCACTACC-AGgtgagttgta ... cattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtttgctcataggaccattcgtctaatgtcgctcagcacacccattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACACTGGTCCAGACTTTTGGGCAGAAGGATCATGTCTGCCTGAAGGAAGGCT
                       gtctaat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgtagagccataacaaaccatgaaccatcagatgtactgccagtgcagtgtggaatgaacctagcctggaaactcatataacggagtttgaaatctttctatcattctattcatgtttgctcataggaccattcgtctaatgtcgctcagcacacccattgttcagGAAGAGAAGGCCATCGAGCGGGGCGTCCTTCCGTTGCTTCGCCGTGCTACACTGGTCCAGACTTTTGGGCAGAAGGATCATGTCTGCCTGAAGGAAGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA