RetrogeneDB ID: retro_dord_344

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_1311:102311..102862(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kin
• Ensembl ID: ENSDORG00000003732
• Aliases: None
• Description: antigenic determinant of rec-A protein [Source:MGI Symbol;Acc:MGI:96676]

Sequence

>retro_dord_344
TGGTACATTCAGTACATAGACAAGGGACTCAGAGACTATTCGGTGGCAACTGGAGCTAAAGAAGAAGCAGGACCTCAACA
ATGAAGAGAAAACTGCCAAGTTTATTGAAGAGCAGATGAGTTGAGGTCTGGAAGGGAAAGAGCAGGAGACCCCTGTTTTC
ACAGAATTCAGCAGAGAAAATTACATTTCATCTGAATGAAGGAGCAGGCAGTTCATCAGGAACATCTTCCAAATCAAGTC
TCTGGGGGCCAAGTGTCCCGAAAACACTGGTGAATGCAGCATCTGTAAAGTAAAAAGACTTTCCAGAGCTCAGCGCAGGC
TGAAGAAAAGAAGAAAAAGAAATCTGTACTCGATGGAATCAGGGAGATTGAAGAGGAAAAGAAAAGAACATCCCAAATGG
ACCCCTGGCTGAAATCACTGTAAAAATTATAACTAAAAAACTTGGCAATAAACATCATAAGAAAAAGGGTATTGTTAAAG
AAGTAATTGATAAGTCAACAGCTGTTGTAAAGCTGATTGAGTCTGGAGATGACCAGAATCACTTAGACAGT

Alignment

ORF - retro_dord_344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.91 %
• Parental protein coverage: 56.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  WYIQYID-RDPETIRRQLELEKKKKQDLDDEEKTAKFIEEQVRRGL-EGKEQETPVFTELSRENDEEKVT
          WYIQYID.RD.ETIR.QLEL..KKKQDL..EEKTAKFIEEQ...GL..GK....P.F......N..EK.T
Retrocopy WYIQYID>RDSETIRWQLEL--KKKQDLNNEEKTAKFIEEQMS*GL>KGKSRR-PLFS----QNSAEKIT

Parental  FNLNKGACSSAGTSSKSS-SLGPSALKTLGSAASVKRKDSS-QSSAQAKEKKKKKSALDEIMEIEEEKKR
          F.LN.GA.SS.GTSSKSS.SLG.......G.....K.K..S.QSSAQA.EKKKKKS.LD.I.EIEEEKKR
Retrocopy FHLNEGAGSSSGTSSKSS<SLGAKCPENTGECSICKVKRLS<QSSAQAEEKKKKKSVLDGIREIEEEKKR

Parental  TSRTDHWLQPEIIVKIITKKLGDKYHKKK-AIVKEVIDKYTAVVKMIDSGDKLKLDQTHLET
          TS..D.WL......K...K.L......K...IVKEVIDK.TAVVK.I.SGD....DQ.HL..
Retrocopy TSQMDPWLKS--L*KL*LKNLAINIIRKR<GIVKEVIDKSTAVVKLIESGD----DQNHLDS

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_344 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004280	1 retrocopy	retro_acar_162,
Cavia porcellus	ENSCPOG00000010515	5 retrocopies	retro_cpor_279, retro_cpor_281, retro_cpor_818, retro_cpor_987, retro_cpor_989,
Dipodomys ordii	ENSDORG00000003732	2 retrocopies	retro_dord_344 , retro_dord_657,
Ficedula albicollis	ENSFALG00000001842	1 retrocopy	retro_falb_26,
Myotis lucifugus	ENSMLUG00000002261	1 retrocopy	retro_mluc_1186,
Rattus norvegicus	ENSRNOG00000026690	1 retrocopy	retro_rnor_2665,
Taeniopygia guttata	ENSTGUG00000002119	1 retrocopy	retro_tgut_9,