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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagagagtttaatcaacattttacattgagatattgtcacactgaattttcaaggggtcatatctgctgttattattatattaaaaaaatatctgctgttgttacag

Basic information

species Zea mays
transcript GRMZM2G004932_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 5'ss of exon 3
GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagagagtttaatcaacattttacattgagatattgtc----acactgaattttcaaggggtcatatctgctgttattattatattaaaaaaatatctgctgttgttacag
||| |||||||| |||||||||||||| || || |||||||||||  || ||| | |  |   |||||| || ||| ||||     |   ||||||| || |  |  || ||||   |||                                   
GCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAGgtaaagcagtgttaatt--atggtttacactgtgatgttgtagtcgatggtgaatttacaggtagctatttctgtgcttacag--------------------------------

upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 5'ss of exon 4
GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagagagtttaatcaacattttacattgagatattgtcacactgaattttcaaggggtcatatctgctgttattattatattaaaaaaatatctgctgttgttacag
||||||||||||| |||| |||||||| ||||||||||| ||||   | |      ||  | ||   ||||    | ||||      |  | |    |  |     |||| | |     || | |                          
GCAGTATTTTGTCGATGAGGATGACACGGTTCCTCAAAAAgtaagt-acaacactctctcctttagccattagcgt-ttgtttattcgtctctcgttgatgaagattctggtttcgcctttttgtag------------------------
















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|213183718|gb|FM190236.1|FM190236
EST:     TGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: TGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|211119333|gb|FL065968.1|FL065968
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|71433707|gb|DR814757.1|DR814757
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|211119334|gb|FL065969.1|FL065969
EST:     GCAGTATTTTGCCNAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCA
genomic: GCAGTATTTTGTC-AATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCA
EST: gi|211119336|gb|FL065971.1|FL065971
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCA
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCA
EST: gi|211119335|gb|FL065970.1|FL065970
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|211118534|gb|FL065953.1|FL065953
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|211119328|gb|FL065963.1|FL065963
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|211119329|gb|FL065964.1|FL065964
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCANAANAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|211119337|gb|FL065972.1|FL065972
EST:     GCAGTATTTTGNCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCANAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|211118531|gb|FL065950.1|FL065950
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCG
EST: gi|211118532|gb|FL065951.1|FL065951
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|211118537|gb|FL065956.1|FL065956
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAG
EST: gi|211119330|gb|FL065965.1|FL065965
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
EST: gi|211273595|gb|FL065975.1|FL065975
EST:     GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG                         GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG
genomic: GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGG

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: 46 (upstream exon), 49 (downstream exon)
Score: 178

GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 221

GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 307

GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 73

GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagaga ... gttgttacagGTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGgtaaaagagagtttaatcaacattttacattgagatattgtcacactgaattttcaaggggtcatatctgctgttattattatattaaaaaaatatctgctgttgttacag

- - - - - - -  TGAAGA
- - - - - - - -  AAGATG