RetrogeneDB ID: retro_dord_694

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5695:55033..55739(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cpsf7
• Ensembl ID: ENSDORG00000000998
• Aliases: None
• Description: cleavage and polyadenylation specific factor 7 [Source:MGI Symbol;Acc:MGI:1917826]

Sequence

>retro_dord_694
CCTCCACGGGCCCGCTCCCCAGATTCTAGTGATTCTGCTGATGGACGAGCCACACCCTGAACCTTGTGCCCTTGTCCACT
CCTGTGGACAACCCCCCCAGCTTGCTTCCTTACTTCAATCGCCCTCCTTCAGCCCTTCCATGGATGGATCTGCCCTCACC
TCCAATTCCACCCCCACCACCTCTCTCCCCAAGTTTTGGGGTTCCTCCTCCACCTCCTGGTATCCTCTACCAGCATCTCA
GGCCCCCTCCTCCTCGATTACTGCCTTATCTTGCCGCACCTCCCCCTGGGTCCGCCCCACCTGCCCTGCGCCTCAATCCA
GTCTTCTCCCCCACTCCAACCCCACCCAATGCTACTGTGGGGCCTCCACCTGAGACTTACATGAAGGCCTCCATACCCGA
TAACCGCCATGGCAGCCGAGAGTGGGGGCCCCCGCCTTCCACAGTGAGAGAAGTGGGATCTGAAGAGATCATGAGACCAA
ACAGAGCAGTTTCTAGCAGTGCCATTTCCAAAGCGGTACCTGCAGCCAGTGCGGGGGGTTGCAGGGAGGTAATCGCGACA
TGGCTCACAGCCATTGCGGTTGTTAAACAGCCCCGGTCTCCAATGATGAGCATTGCCCAGTCCTTGTCTCCTGCTTAAAG
CGCTGTTTAATGCATCATGGCCTCCAGGCCAAGTCCTCCAGTGTGGGTACCAGTGGGAGCTCTTCC

Alignment

ORF - retro_dord_694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.55 %
• Parental protein coverage: 55.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPRAHSRDSSDSADGRATPSENLVPSSARVDKPP-SVLPYFNRPPSALPLMGLPPPPIPPPPPLSSSFGV
          PPRA.S.DSSDSADGRATP...L.P.......PP.S.LPYFNRPPSALP.M.LP.PPIPPPPPLS.SFGV
Retrocopy PPRARSPDSSDSADGRATP-*TLCPCPLLWTTPP<SLLPYFNRPPSALPWMDLPSPPIPPPPPLSPSFGV

Parental  PPPPPGIHYQHLMPPPPRLPPHLAVPPPGAVPPALHLNPAFFP---PPNATVGPPPDTYMKASTPYNHHG
          PPPPPGI.YQHL.PPPPRL.P.LA.PPPG..PPAL.LNP.F.P...PPNATVGPPP.TYMKAS.P.N.HG
Retrocopy PPPPPGILYQHLRPPPPRLLPYLAAPPPGSAPPALRLNPVFSPTPTPPNATVGPPPETYMKASIPDNRHG

Parental  SRDSGPPPSTVSEAEFEEIMKRNRAISSSAISKAVSGASAGDYSDAIETLLTAIAVIKQSR-VSNDERCR
          SR..GPPPSTV.E...EEIM..NRA.SSSAISKAV..ASAG.....I.T.LTAIAV.KQ.R.VSNDE.C.
Retrocopy SREWGPPPSTVREVGSEEIMRPNRAVSSSAISKAVPAASAGGCREVIATWLTAIAVVKQPR<VSNDEHCP

Parental  VLISSLKDCL--HGIEAKSYSVGASGSSS
          VL.S.LK.CL..HG..AKS.SVG.SGSSS
Retrocopy VLVSCLKRCLMHHGLQAKSSSVGTSGSSS

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_694 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000998	1 retrocopy	retro_dord_694 ,