RetrogeneDB ID: retro_dord_261

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6813:1856256..1856955(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ppp1cc
• Ensembl ID: ENSDORG00000010484
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, gamma isoform [Source:MGI Symbol;Acc:MGI:104872]

Sequence

>retro_dord_261
GACCTTCTGGGGCTGTTTGAATATGGTGGCTTCCTTCCAGAGAGCAACTACTTCTTCCCGGGGGACTATGTGGACCGGGG
CAAGCAGTCTTTGGAGACCATCTGCCTGCTGCTGGCCTATAAGATAAAATACCCTGAGAATTTCTTCCTGCTCTGTGGGA
ACCATGAGTGTGCCAGCATCAACCGCATCTATGGCTTCTATGATGAATGCAAGAGATGCTACAATATCAAACTGTGGAAA
ACTTTCACTGACTGCTTCAACTGCCTGCCCATCATAGCCATTGTAGATGAGAAGATCTTCTGCTGCCATGGAGGCCTGTC
CCCAGACTTGCAGTCCATGGAGCAGATTCGGCGTATCATGCGGCCCACAGATGTGCCTGACCAGGGCCTGCTGTGTGACT
TGCTGTGGTCTGACCCTGACAAGGATGTGCAGGGCTGGGGCGAGAATGACTGAGGTGTCTCCTTTACCTTTGGGGCTGAG
GTAGTGGCCAAGTTCCTACACAAGCACGACTTGGACCTCATCTGCAGGGCACGCCAGGTGGTAGAAGATGGTTATGAGTT
CTTTGCCAAGTGGCAGCTGGTGACACTTTTCTCAGCTCCCAATTACTGTGGCAAGTTTGACAATTCTGGTGCCATGATGA
GCGTGGATGAGCCCCTCATGTGCTCCTTCCAGATCCTCAAGCCCACTGATAAGAACAAG

Alignment

ORF - retro_dord_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.7 %
• Parental protein coverage: 69.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDEC
          DLL.LFEYGGF.PESNY.F.GDYVDRGKQSLETICLLLAYKIKYPENFFLL.GNHECASINRIYGFYDEC
Retrocopy DLLGLFEYGGFLPESNYFFPGDYVDRGKQSLETICLLLAYKIKYPENFFLLCGNHECASINRIYGFYDEC

Parental  KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
          KR.YNIKLWKTFTDCFNCLPI.AIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
Retrocopy KRCYNIKLWKTFTDCFNCLPIIAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD

Parental  KDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
          KDV.GWGEND.GVSFTFGAEVVAKFLHKHDLDLICRA.QVVEDGYEFFAK.QLVTLFSAPNYCG.FDN.G
Retrocopy KDVQGWGEND*GVSFTFGAEVVAKFLHKHDLDLICRARQVVEDGYEFFAKWQLVTLFSAPNYCGKFDNSG

Parental  AMMSVDETLMCSFQILKPAEKKK
          AMMSVDE.LMCSFQILKP..K.K
Retrocopy AMMSVDEPLMCSFQILKPTDKNK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_261 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Dipodomys ordii	ENSDORG00000010484	2 retrocopies	retro_dord_260, retro_dord_261 ,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Vicugna pacos	ENSVPAG00000008411	1 retrocopy	retro_vpac_540,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,