Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcccgcatccccgatctggttgtatctgttttccccgtgagaggtatctgatgctgctgcaaatgtctgtgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATGTGGCGCGGGTGGAGAAGATGGAGGGCGACGGGCGTGGCAGCGTGCGGGT

Basic information

species Zea mays
transcript GRMZM5G871463_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g32620.3 (Oryza sativa), 3'ss of exon 1
------------------------------gtaatttcccgcatccccgatctggtt------------gtatctgttttccccgtgagaggtatctgatgctgctgcaaatgtctgtgccggga--agTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATGTGGCGCGGGTGGAGAAGATGGAGGGCGACGGGCGTGGCAGCGTGCGGGT
                               | || |||||  | |  ||| |   |              |          | | | | || |    ||| |||||    |   || |   |||  |||||| |||||||||||||||||| ||  ||||||||||||||||||||| ||||||||||||||||||||||||   |||||||| || |||||||||||
gtcgtacgaggtaacgtgcctccccgtcctctgatctcccgggttcttgatttccctcgggcgagagagaaagaaaaaaaatctgaggggggcaagcaatg-tgctgttgtttggtgggattggagcagTGGGGGACTGCGTGCTGATGCGGCCGGTGGACTCGGACAACCAGCCGTACGTGGCGCGGGTGGAGAAGATGGAGCTGGACGGGCGCGGGAGCGTGCGGGT

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 1
--------------------gtaatttcccgcatccccgatctggttgtatctgt------------tttccccgtgagaggtatctgatgctgctgcaaatgtctgtgccggga--agTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATGTGGCGCGGGTGGAGAAGATGGAGGGCGACGGGCGTGGCAGCGTGCGGGT
                     | || |||||  | |  ||| |   |    |                    | | | | || |    ||| |||||    |   || |   |||  |||||| |||||||||||||||||| ||  ||||||||||||||||||||| ||||||||||||||||||||||||   |||||||| || |||||||||||
gtaacgtgcctccccgtcctctgatctcccgggttcttgatttccctcgggcgagagagaaagaaaaaaaatctgaggggggcaagcaatg-tgctgttgtttggtgggattggagcagTGGGGGACTGCGTGCTGATGCGGCCGGTGGACTCGGACAACCAGCCGTACGTGGCGCGGGTGGAGAAGATGGAGCTGGACGGGCGCGGGAGCGTGCGGGT
















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|211489995|gb|FL137478.1|FL137478
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211489991|gb|FL137474.1|FL137474
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211492880|gb|FL137490.1|FL137490
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211487121|gb|FL137471.1|FL137471
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211489996|gb|FL137479.1|FL137479
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCKTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211490003|gb|FL137486.1|FL137486
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|26456797|gb|CA828380.1|CA828380
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211492882|gb|FL137492.1|FL137492
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211490002|gb|FL137485.1|FL137485
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211489990|gb|FL137473.1|FL137473
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211489989|gb|FL137472.1|FL137472
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211489992|gb|FL137475.1|FL137475
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211492881|gb|FL137491.1|FL137491
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211492878|gb|FL137488.1|FL137488
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211489999|gb|FL137482.1|FL137482
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211492879|gb|FL137489.1|FL137489
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211492877|gb|FL137487.1|FL137487
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211490001|gb|FL137484.1|FL137484
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211489993|gb|FL137476.1|FL137476
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTA--                         T----GACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211489997|gb|FL137480.1|FL137480
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
EST: gi|211490000|gb|FL137483.1|FL137483
EST:     TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATG                         TGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG
genomic: TAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATG

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: 48 (upstream exon), 49 (downstream exon)
Score: 278

ACCCCTCCATATCCTCGCTCCACGGTCATGGCGAAGACGAAGCAGGGAAATAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATGTGGCGCGGGTGGAGAAGATGGAGGGCGACGGGCGTGGCAGCGTGCGGGT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 54

ACCCCTCCATATCCTCGCTCCACGGTCATGGCGAAGACGAAGCAGGGAAATAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATGTGGCGCGGGTGGAGAAGATGGAGGGCGACGGGCGTGGCAGCGTGCGGGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 48

ACCCCTCCATATCCTCGCTCCACGGTCATGGCGAAGACGAAGCAGGGAAATAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATGTGGCGCGGGTGGAGAAGATGGAGGGCGACGGGCGTGGCAGCGTGCGGGT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 109

ACCCCTCCATATCCTCGCTCCACGGTCATGGCGAAGACGAAGCAGGGAAATAAGGACGTGGATTCGTACACCATCGGCGGCACCAACAAGGTCGTCTATGgtaatttccc ... tgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATGTGGCGCGGGTGGAGAAGATGGAGGGCGACGGGCGTGGCAGCGTGCGGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttttccccgtgagaggtatctgatgctgctgcaaatgtctgtgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATGTGGCGCGGGTGGAGAAGATGGAGGGCGACGGGCGTGGCAGCGTGCGGGT
                     atctgat  putative branch site (score: 109)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttcccgcatccccgatctggttgtatctgttttccccgtgagaggtatctgatgctgctgcaaatgtctgtgccgggaagTGGGAGACTGCGTGCTGATGCGGGCGTCGGACTCGGACAACCAGCCGTATGTGGCGCGGGTGGAGAAGATGGAGGGCGACGGGCGTGGCAGCGTGCGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG