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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccccccccccccccgacctctactatacataattttagtgtttcttatgttatacatcttgtattatcctcttattttttacatcgctattgcttggcccatggtatttagttaaatctaatgttttgtatctgttcaaggag

Basic information

species Zea mays
transcript GRMZM2G376727_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G376727_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g01307.2 (Oryza sativa), 5'ss of exon 3
TGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccccccccccccccgacctctactatacataattttagtgtttcttatgttatacatcttgtattatcctcttattttttacatcgctattgcttggcccatggtatttagttaaatctaatgttttgtatctgttcaaggag
|||| | ||  ||| |||| |||||||||||  |||||||||||| || |||||||| ||  ||||||| || ||||||||||||||| |||| ||||||||     |     | |   |  || | |   |     || || ||   || || | ||| | |     |  | | ||  |||  ||   || |||     ||      | ||||   || ||                            
TGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctgttacacttacacacttttttaa-----aacttcagctcttttttttttaaagaaaa-atgctgttctgctatgcttgcaattgct--caattttttttttgtat--ggtgaag---------------------------
















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|21987232|gb|BQ778760.1|BQ778760
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
EST: gi|87156435|gb|DY401224.1|DY401224
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|37377085|gb|CF625114.1|CF625114
EST:     CACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTTCTCTTCAGGAG                         GCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCC
genomic: CACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaaggagGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCC
EST: gi|211354951|gb|FL243591.1|FL243591
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACT
EST: gi|9255123|gb|BE345591.1|BE345591
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
EST: gi|24769483|gb|CA404612.1|CA404612
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCT
EST: gi|60354184|gb|DN221157.1|DN221157
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|7137614|gb|AW499182.1|AW499182
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|211354953|gb|FL243593.1|FL243593
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
EST: gi|60346405|gb|DN213378.1|DN213378
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|38671702|gb|CD219303.2|CD219303
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|15590113|gb|BI674729.1|BI674729
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
EST: gi|211340832|gb|FL479597.1|FL479597
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|149106143|gb|EE291820.2|EE291820
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
EST: gi|24765720|gb|CA400879.1|CA400879
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|30706031|gb|CD059006.1|CD059006
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|60356569|gb|DN223542.1|DN223542
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|60355754|gb|DN222727.1|DN222727
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|78107599|gb|DV526017.1|DV526017
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
EST: gi|78080233|gb|DV508645.1|DV508645
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
EST: gi|211379488|gb|FL165247.1|FL165247
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
EST: gi|74243940|gb|DT651854.1|DT651854
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|211130310|gb|FL066377.1|FL066377
EST:     TGTTCCCACAAAGACTGCTCTTSAGGAG                         GCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCC
genomic: TGTTCCCACAAAGACTGCTCTT---CAGgtcccccccc ... gttcaaggagGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCC
EST: gi|15053451|gb|BI358996.1|BI358996
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|7135675|gb|AW498208.1|AW498208
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCNCAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|60347341|gb|DN214314.1|DN214314
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|211130311|gb|FL066378.1|FL066378
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAG                         GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagG---CCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTT
EST: gi|16919381|gb|BM074163.1|BM074163
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|60347158|gb|DN214131.1|DN214131
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|76285099|gb|DV024667.1|DV024667
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|31611983|gb|CD568605.1|CD568605
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg
EST: gi|89249519|gb|DY621305.1|DY621305
EST:     GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGGAG                       
genomic: GTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTC---AGgtcccccccc ... gttcaagg

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: 17

TGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGGTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

TGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGGTAA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 18

TGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGGTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20

TGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACTGCTCTTCAGgtcccccccc ... gttcaaggagGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGGTAA