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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggctgccatcctttccactcaaccctatatgtcaacttgcaaaacattctcagagttcgctgtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTTGATCTT

Basic information

species Zea mays
transcript GRMZM2G020976_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g40030.1 (Oryza sativa), 3'ss of exon 8
--------gtacggctgccatcctttccactcaacc----ctatatgtcaacttgcaaaacattctcagagttcgctgtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTTGATCTT
        |   |  | |  | | |||||||| |||     |  | ||    ||  |      | ||| | ||  || |||||  |||||||||||||||| |||||||| ||||| || |||||||| |||||||||||||| 
gtataacagcctgcatccagttccttccactccaccaaacttgcaagttgttttttagtgtcctttcatatttacctttttctgcagGATTTCTTCACCGTCGGAATTGGCTGGGTTCTGTTTGGTGGGCTTCCTTTTGATCTG
















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|74233566|gb|DT641480.1|DT641480
EST:     ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAG                         GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
genomic: ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
EST: gi|166440982|gb|EG122752.1|EG122752
EST:     ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAG                         GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGNGGTCTT
genomic: ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTT
EST: gi|78115508|gb|DV533896.1|DV533896
EST:     ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAG                         GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
genomic: ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
EST: gi|71420100|gb|DR805010.1|DR805010
EST:     ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAG                         GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
genomic: ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
EST: gi|110210988|gb|EC892885.1|EC892885
EST:     ACACAATCCTGAATTTTGCACTCACACAATCTATGTGTGGCAACTTGAAG                         GATTTTTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
genomic: ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
EST: gi|40303781|gb|CK348168.1|CK348168
EST:     ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAG                         GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
genomic: ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
EST: gi|71298000|gb|DR784969.1|DR784969
EST:     ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAG                         GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
genomic: ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
EST: gi|89760089|gb|DY688655.1|DY688655
EST:     ACACAATCCTGAATTCTGCACTCACCCAATCTATGTGTGGCAACTTGAAG                         GATTTTTTCCCCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT
genomic: ACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTT

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), 44 (downstream exon)
Score: 72

TCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTTGATCTT


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 185

TCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTTGATCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

TCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTTGATCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

TCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCAACTTGAAGgtacggctgc ... gtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTTGATCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcaaccctatatgtcaacttgcaaaacattctcagagttcgctgtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTTGATCTT
                                       ttcgctgtttcttt  CT-rich tract
                        aaaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggctgccatcctttccactcaaccctatatgtcaacttgcaaaacattctcagagttcgctgtttctttagGATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGTCTTCCTTTTGATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG