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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgcgcgcgcgcgcgttcctccgattcgccgcgcccgtgcctcggattcgcacgattcggtggcgttcgtgccggaaacttgtggtcctggagg...

Basic information

species Zea mays
transcript GRMZM2G008259_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008259_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 5'ss of exon 1
-------------------------------------------------------------------ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgcgcgcgcgcgc-gttcctccgattcgccgcgcccgtgcctcggattcgcacgattcg-gtggcgttcgtgccggaaacttgtggtcctggagg
                                                                   | ||||||||||||||||||||||| ||||||||||||||  |   |  |    |||||||||||||||||| | || | |||| ||| |   | |||  |  |  || |  | || ||  ||||||  | ||  
TTGCTGATGAGTGGTGAATGAGTGGCTGATTTTGGTTTGGTTGGATTTTTTTTTGTTTCTTTTGCAGATGTGGAGAAGTTCTACCAGCAGTGCGACCCAGgtgagcttcccttcctgtttagttcctccgattcgccgctctcggggctcgaatttgtgtgtttcttgatgttttagctcggggaagatgtggtttttga--

upper sequence: GRMZM2G008259_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g14010.1 (Oryza sativa), 5'ss of exon 2
ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgcgcgcgcgcgc-gttcctccgattcgccgcgcccgtgcctcggattcgcacgattcg-gtggcgttcgtgccggaaacttgtggtcctggagg
| ||||||||||||||||||||||| ||||||||||||||  |   |  |    |||||||||||||||||| | || | |||| ||| |   | |||  |  |  || |  | || ||  ||||||  | ||  
ATGTGGAGAAGTTCTACCAGCAGTGCGACCCAGgtgagcttcccttcctgtttagttcctccgattcgccgctctcggggctcgaatttgtgtgtttcttgatgttttagctcggggaagatgtggtttttga--
















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|60341456|gb|DN208429.1|DN208429
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|101398089|gb|EB820919.1|EB820919
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|149070148|gb|EE158549.2|EE158549
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|76916780|gb|DV166549.1|DV166549
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|76290977|gb|DV030545.1|DV030545
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|76281879|gb|DV021447.1|DV021447
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|22819609|gb|BU499699.1|BU499699
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|28910319|gb|CB331379.1|CB331379
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|148930178|gb|EC872565.2|EC872565
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|22819406|gb|BU499496.1|BU499496
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|78114017|gb|DV532406.1|DV532406
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|9794347|gb|BE552655.1|BE552655
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|149075823|gb|EE164362.2|EE164362
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|78118666|gb|DV537050.1|DV537050
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|149106607|gb|EE188500.2|EE188500
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|149008353|gb|EE040506.2|EE040506
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|50338834|gb|CO533960.1|CO533960
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|74236627|gb|DT644541.1|DT644541
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|26559804|gb|CA832039.1|CA832039
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|71766893|gb|DR964830.1|DR964830
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|13490681|gb|BG517445.1|BG517445
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
EST: gi|78120146|gb|DV538530.1|DV538530
EST:     ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAG                         AGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA
genomic: ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGA

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: 457

ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGAACTTGCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCAGCTCTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGAACTTGCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCAGCTCTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGAACTTGCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCAGCTCTGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 94

ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgc ... ttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGAACTTGCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCAGCTCTGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGTGGAGAAGTTCTACCAGCAGTGTGACCCAGgtgagctcgcgcgcgcgcgcgttcctccgattcgccgcgcccgtgcctcggattcgcacgattcggtggcgttcgtgccggaaacttgtggtcctggagg

- GTGGAG
-  TGGAGA
- - GGAGAA
- - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcgcc