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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatagcaaatcacacatataggcatagcacatagcagtgtattcagttgaccagttctaagttcgcaaactaactaactgtgatttaacacttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAAAGCCACCTGTTCTACAATATGACATCGCTCCTATGGAAGGGTATTCAGC

Basic information

species Zea mays
transcript GRMZM2G140994_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140994_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g18100.1 (Oryza sativa), 3'ss of exon 1
--ccatagcaaatcacacatataggcatagcacatagcagtgtatt--cagttgaccagttctaagttcgcaaactaactaactgtgatttaacacttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAAAGCCACCTGTTCTACAATATGACATCGCTCCTATGGAAGGGTATTCAGC
  ||||     ||  |  | |    | ||    || |   || | |  ||||   |  |||| |  |    || | |  | |  ||  ||      | |||||| |  | ||| ||   ||||||||| ||||  | |||||||||||||||||||  ||| | |||| ||| ||| |||| ||| |||||||||| || ||||
ccccatt-tggatttcctacaccttc-tattttattgttttgaagttacagtctgctggttccacctgactaagcaagatgatcgttgttggtt--tgttgcagTACTGTGACCTGACACGCTTCTTCCTGTCGGCTTTCTACCACTTGAGCGAAACTCACTTCTTCTTCAACATGTCATCTCTCTTATGGAAGGGCATCCAGC
















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|71765692|gb|DR963629.1|DR963629
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|74240023|gb|DT647937.1|DT647937
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|31353863|gb|CD438220.1|CD438220
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|149080892|gb|EE169974.2|EE169974
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|91052458|gb|EB162876.1|EB162876
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|211391130|gb|FK982151.1|FK982151
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|211391127|gb|FK982148.1|FK982148
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|211388500|gb|FK982147.1|FK982147
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|71447514|gb|DR828564.1|DR828564
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCAAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|148949022|gb|EC894444.2|EC894444
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|148937158|gb|EC881336.2|EC881336
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
EST: gi|211388491|gb|FK982138.1|FK982138
EST:     TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAG                         AATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA
genomic: TCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAA

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: 36 (upstream exon), 46 (downstream exon)
Score: 24

GCTCGCCGGCAACGCGCTCATCTATCTCCGTCCCGGGGCGCTCGACGGGATCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAAAGCCACCTGTTCTACAATATGACATCGCTCCTATGGAAGGGTATTCAGC


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 39

GCTCGCCGGCAACGCGCTCATCTATCTCCGTCCCGGGGCGCTCGACGGGATCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAAAGCCACCTGTTCTACAATATGACATCGCTCCTATGGAAGGGTATTCAGC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 22

GCTCGCCGGCAACGCGCTCATCTATCTCCGTCCCGGGGCGCTCGACGGGATCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAAAGCCACCTGTTCTACAATATGACATCGCTCCTATGGAAGGGTATTCAGC


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 47

GCTCGCCGGCAACGCGCTCATCTATCTCCGTCCCGGGGCGCTCGACGGGATCCTGCCCTCTGTCACACGCGTCTCCTTCAATCCGCGGCTCATCGTCGAGgtacccaatc ... acttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAAAGCCACCTGTTCTACAATATGACATCGCTCCTATGGAAGGGTATTCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgaccagttctaagttcgcaaactaactaactgtgatttaacacttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAAAGCCACCTGTTCTACAATATGACATCGCTCCTATGGAAGGGTATTCAGC
                                            cactttt  CT-rich tract
                                    tgatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatagcaaatcacacatataggcatagcacatagcagtgtattcagttgaccagttctaagttcgcaaactaactaactgtgatttaacacttttgcagAATGGCGACTTGGTGCGCTTCTTCTTGTCACCATTCTACCACTTGAGCGAAAGCCACCTGTTCTACAATATGACATCGCTCCTATGGAAGGGTATTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - tcacaca
- - - - - - - - - - - - - -gcacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgatt