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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgctcctgtgaatgatgctaatgttaatttttttcccgtttgttattacaccaacaacaatctgtctgccatgcttgcaacttgcttgtaccgatgatagtttcaaaccctttcctctcccctcctctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC

Basic information

species Zea mays
transcript GRMZM2G142806_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142806_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 9
gtaagtcg----ctcctgtgaatgatgctaatgttaattttt--ttcccgtttgt-----tattacaccaacaaca-atctgtctgccatgcttgcaac-ttgcttgtaccgatgatagt-ttcaaacccttt----------cctctcccctcctctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC
|||||| |      ||  ||| || |  ||||  |  ||||    | | || | |     | || ||          |      |||  |  |  |||  || || ||    ||  || | | |||  || ||           |||||      |||     ||||||| ||||||||| |||| || ||||||||||||||||| |||||||| |||||||| || ||||||| |||||| ||||| ||||| |||||||| |
gtaagttgaagtaccccttgactgttcataattatttttttcaacttcagtgtatgcaagtgttgcatgcctggtgcaggcaaatgcagttttcacaatgtttctggtgtaaatactaatgtccaagtccattgtaattaagttctctctttatttctacctcagTGGTCAGACAAGCTGAAGAAACTTGATTTTCAAGAGATGGTCATGTTCCTTCAGCACCTTCCGACGAGGAACTGGGCTCACCATGAGCTTGAGATGGTGC

upper sequence: GRMZM2G142806_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G03200.1 (Glycine max), 3'ss of exon 9
gtaagtcgctcctgtgaatgatgctaatgttaatttttttcccgtttgttattacaccaacaacaatctgtctgccatgcttgcaacttgcttgtaccgatgatagtttcaaaccctttcctctcccctcctctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC
                           ||  | |||||| || ||        ||  |  || || | ||||    |||||| | | || |   ||      ||| | || || | || |   |    |  ||      ||||||| |||||||| |||||||| ||||| ||||||||||| |||||||| |||||||| || || | || |||| | || || ||||| |||||||| |
---------------------------tgcaacttttttgccagtaca----cacttctgcaccactttgtc---aatgctt-ctatttccccctaggatgaatattctctaatctttacaattgtttttatc------agTGGTCTGACAAGCTCCAGAAGCTTGATTTCCAAGAGATGGTAATGTTCCTTCAGCACCTTCCAACTAAGAACTGGACTCAACAGGAGCTCGAGATGGTAC

upper sequence: GRMZM2G142806_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtcgctcctgtgaatgatgctaatgttaatttttttcccgtttgttattacaccaacaacaatctgtctgccatgcttgcaa---cttgcttgtaccgatgat-agtttcaaaccctttcctctcccctcctctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC
                                                  | |  | | |  | ||  ||   |     |||| ||    || ||| ||   |  |  ||  |||||  |       | |  |   |  ||| ||||||| ||  ||||| ||||||| ||||||||||| ||||| ||||||||||| ||||| || ||    | |||| |  |||| ||||| || |||||  
----------------------------------------gtaagcaaacactgaatcgaatataacttgc--gttggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaaca-atgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT

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|160481316|gb|EY254259.1|EY254259
EST:     ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACG                         TGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
genomic: ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
EST: gi|149073693|gb|EE161998.2|EE161998
EST:     ACTATCTGCCAGATTTTTTCGTGTACATATCGGCTAGTTTTTTGCTGACG                         TGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
genomic: ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
EST: gi|71426203|gb|DR807253.1|DR807253
EST:     ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACG                         TGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
genomic: ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
EST: gi|166615792|gb|EG212745.1|EG212745
EST:     CTCGTGTACATATCGGCTAGTTTTTTGCTGACG                         TGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAG
genomic: CTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAG
EST: gi|211467151|gb|FL432006.1|FL432006
EST:     ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACG                         TGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
genomic: ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
EST: gi|32839236|gb|CD978917.1|CD978917
EST:     ACATATCGGCCAGTTTTTTGCTGACG                         TGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
genomic: ACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
EST: gi|60355822|gb|DN222795.1|DN222795
EST:     ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACG                         TGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
genomic: ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
EST: gi|86468229|gb|DY234599.1|DY234599
EST:     ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACG                         TGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
genomic: ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
EST: gi|60394994|gb|DN227863.1|DN227863
EST:     ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACG                         TGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG
genomic: ACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTG

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: 73

ACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 52

ACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 51

ACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

ACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGACGgtaagtcgct ... tctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcttgtaccgatgatagtttcaaaccctttcctctcccctcctctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC
                    tttcaaaccctttcct  CT-rich tract
                atagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgctcctgtgaatgatgctaatgttaatttttttcccgtttgttattacaccaacaacaatctgtctgccatgcttgcaacttgcttgtaccgatgatagtttcaaaccctttcctctcccctcctctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG