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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtataacctccatgtaataatctcgtttttcaacaatactttcttaataacaacaacaaaaaatcataatgtcacctgtttgactatcttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG

Basic information

species Zea mays
transcript GRMZM5G871336_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871336_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g05830.1 (Oryza sativa), 3'ss of exon 1
ttgtataacctccatgtaataatctcgtttttcaacaatactttcttaataacaacaacaaaaaatcataatgtcacctgtttgactat--cttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG
   || |   | | |   || ||||||     | | | |  |   || |           |       |         |   ||  | |  ||| | || |||| || |  ||||| || || ||||||||| | || ||||| |||||||||||||||||||||||||||||||| ||||||||||
aattaaagattactttatatgatctcgaaa--cgatactgataatttgagtggtttggatagggcaggtggcactgtttcactggttgttgcttgcgtgtagGCTCTCAACTCCAATTCGCAACGTCTTCAGCTGCTGCAGCAGTTGTTTGCTGACATCGCATTGAAGGTGGATGACCGCGCTCGAG
















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|71430125|gb|DR811175.1|DR811175
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211068146|gb|FL037286.1|FL037286
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070875|gb|FL037292.1|FL037292
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|71432140|gb|DR813190.1|DR813190
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211068145|gb|FL037285.1|FL037285
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070876|gb|FL037293.1|FL037293
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070877|gb|FL037294.1|FL037294
EST:     CCGACCGCCTCGAGGSSCTCTCCCTCGAGATCGAGCGCAASSTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211073615|gb|FL037307.1|FL037307
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|71311972|gb|DR792494.1|DR792494
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|148950551|gb|EC896128.2|EC896128
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070883|gb|FL037300.1|FL037300
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|13381878|gb|BG458553.1|BG458553
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCATTTGNNNNNN
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070880|gb|FL037297.1|FL037297
EST:     CCGACCGCCTCGAGGSSCTCTCCCTCGAGATCGAGCGCAASSTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|93012464|gb|EB637984.1|EB637984
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070870|gb|FL037287.1|FL037287
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211073617|gb|FL037309.1|FL037309
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070874|gb|FL037291.1|FL037291
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|149059964|gb|EE157094.2|EE157094
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|149045945|gb|EE047943.2|EE047943
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|94474109|gb|EB703067.1|EB703067
EST:     ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070882|gb|FL037299.1|FL037299
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070884|gb|FL037301.1|FL037301
EST:     CCGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211070878|gb|FL037295.1|FL037295
EST:     CCGACCGCCTCGAGGSSCTCTCCCTCGAGATCGAGCGCAASSTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
EST: gi|211073610|gb|FL037302.1|FL037302
EST:     CCGACCGCCTCGAGGCGCTCTCCCTCGAGATCGAGCGCAAGCTGCACAAG                         GCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT
genomic: ACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCT

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: 43 (upstream exon), 49 (downstream exon)
Score: 33

GCGCCGACGATCACCTCAGGCGTGCGCGGATATGGGGCGCCGCGGCTCCTACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG


Block sizes: 33 (upstream exon), 47 (downstream exon)
Score: 28

GCGCCGACGATCACCTCAGGCGTGCGCGGATATGGGGCGCCGCGGCTCCTACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 14

GCGCCGACGATCACCTCAGGCGTGCGCGGATATGGGGCGCCGCGGCTCCTACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG


Block sizes: 31 (upstream exon), 40 (downstream exon)
Score: 14

GCGCCGACGATCACCTCAGGCGTGCGCGGATATGGGGCGCCGCGGCTCCTACGACCGCCTCGAGGCGCTCTCCCTGGAGATCGAGCGCAAGCTGCACAAGgtaacccacc ... ttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaataacaacaacaaaaaatcataatgtcacctgtttgactatcttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG
                                        ctatcttcc  CT-rich tract
           aacaaaaaatcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtataacctccatgtaataatctcgtttttcaacaatactttcttaataacaacaacaaaaaatcataatgtcacctgtttgactatcttccatgcagGCCCTGATGTCCAACTCACAGCGTCTTCAGATACTTCAGCAATTGTTTGCTGACATCGCATTGAAGGTGGATGATCGCGCTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - -ctccatg
- - - - - - - - - - - - - - - - caacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - caacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacctgt