RetrogeneDB ID: retro_dord_333

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_120610:691..1462(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dnaja4
• Ensembl ID: ENSDORG00000005972
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 4 [Source:MGI Symbol;Acc:MGI:1927638]

Sequence

>retro_dord_333
GGCAAAAAAAGAGGGGGGACAGTGGAGTGCTGTCCCTACTGCCGAGGTACTGGAATGTAAATACAAATTCATCAGATAGG
ACCTGGAACGGTTCAGCATATTCAGGTGTGCGTGGAGTGCTAGGGCCATAGAAAAAGGATCAGTCCTAAAAATAGATATA
AAAGCTGTAATGGAAGGAACACAGTTCAAGAGAAGATGATTCTGGATGTTCATATTGACAAAGGCATGAAAAATGGCCAG
AAGATAACATTCCATGATGAAGGAGACCAAGAACTAGGATTGGAGCCTGGAGATATCATCATTGTATCAGATCAGAAGGA
CTATGCTATTTTTATGTGACAAAGATAAGATTTTTTTATGTGTATGGACATACAACTGGTTGAAGCACTGTGTGGCTTCC
AATAGCCAATCTCCACTCTTGACAACCAAACCATAGTCATTGCTTCTCATCCAGGTCAGATTGTCAAGCTGGGAGATATC
AAGAGTGTGCTAAATAAAGGCATGCCAATTTATTGACAACCATATGAAAAGGGGCACTTAATCATTGAGTTTAAGGTGAA
CTTTCCTGAAAACAGCTTCCTCTCTCCTGATAAACTCTCTTTGCTGGAAAAATTCCTTCTTGAGAGGAAGGAAGTAGAAG
AGACTGATAAAATGGATCAGGTAGAACTGGTACACTTTGATCCAAATCAGGAAAGATGGTGCCATTATAATGGAGAAGCT
TACAAGGATGATGAACATCACCCTAGAGGTGGTGTTCCGTGTCAAACCTCA

Alignment

ORF - retro_dord_333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.33 %
• Parental protein coverage: 99.22 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKK--GSVEKCPLCKGRGMQIHIQQIGPGMVQQIQTVCIECKGQGERINPKDRCETCSGAKVTREKKIIE
          GKK..G.VE.CP.C.G.GM.I.I.QIGPG.VQ.IQ.VC.EC.G...RI.PK.R...C.G.....EK.I..
Retrocopy GKKRGGTVECCPYCRGTGM*IQIHQIGPGTVQHIQ-VCVEC*GHRKRISPKNRYKSCNGRNTVQEKMILD

Parental  VHGERCMKDGQKILFHGEGDQEPELEPGDVIIVLDQKDHSVFQRRGHDLIMKMKIQLSEALCGFKKTIKT
          VH....MK.GQKI.FH.EGDQE..LEPGD.IIV.DQKD...F.....D..M.M.IQL.EALCGF...I.T
Retrocopy VHIDKGMKNGQKITFHDEGDQELGLEPGDIIIVSDQKDYAIFM*QR*DFFMCMDIQLVEALCGFQ*PIST

Parental  LDDRVLIITSKSGEVMKHGDLKCVRNEGMPIYKAPLERGALILQFLVVFPDKQWLSLEKLPQLEALLPPR
          LD.....I.S..G...K.GD.K.V.N.GMPIY..P.E.G.LI..F.V.FP....LS..KL..LE..L..R
Retrocopy LDNQTIVIASHPGQIVKLGDIKSVLNKGMPIY*QPYEKGHLIIEFKVNFPENSFLSPDKLSLLEKFLLER

Parental  QKVRVTEDMDQVELKEFNPSEQNWRQHR-EAYEEDDDGPRAGVQCQTA
          ..V..T..MDQVEL..F.P....W.....EAY..D...PR.GV.CQT.
Retrocopy KEVEETDKMDQVELVHFDPNQERWCHYNGEAYKDDEHHPRGGVPCQTS

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_333 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 10 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012576	1 retrocopy	retro_amel_1659,
Dipodomys ordii	ENSDORG00000005972	4 retrocopies	retro_dord_245, retro_dord_280, retro_dord_333 , retro_dord_533,
Echinops telfairi	ENSETEG00000004320	4 retrocopies	retro_etel_1010, retro_etel_1031, retro_etel_1067, retro_etel_608,
Macropus eugenii	ENSMEUG00000015982	4 retrocopies	retro_meug_1059, retro_meug_1893, retro_meug_292, retro_meug_624,
Microcebus murinus	ENSMICG00000008789	6 retrocopies	retro_mmur_1242, retro_mmur_1460, retro_mmur_39, retro_mmur_482, retro_mmur_496, retro_mmur_578,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
Otolemur garnettii	ENSOGAG00000006752	5 retrocopies	retro_ogar_1760, retro_ogar_1985, retro_ogar_221, retro_ogar_2656, retro_ogar_841,
Ochotona princeps	ENSOPRG00000007594	1 retrocopy	retro_opri_1028,
Tupaia belangeri	ENSTBEG00000009268	9 retrocopies	retro_tbel_2276, retro_tbel_2308, retro_tbel_2790, retro_tbel_2831, retro_tbel_3242, retro_tbel_4322, retro_tbel_4735, retro_tbel_772, retro_tbel_796,
Tarsius syrichta	ENSTSYG00000008600	1 retrocopy	retro_tsyr_1752,