RetrogeneDB ID: retro_dord_447

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_19474:11522..12053(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ppih
• Ensembl ID: ENSDORG00000016152
• Aliases: None
• Description: peptidyl prolyl isomerase H [Source:MGI Symbol;Acc:MGI:106499]

Sequence

>retro_dord_447
ATGATGGTGGCAAATGTAAGCCCCATCAACCCCATCATGTTATTTGATGTTAGCATTAGTGGTCAGGAGGTTGGACACAT
GAAGATTGAGCTGTTTGCAGATGTTGTGCTTCAGACAACCGAGAACTTTAGGCAGTTCTGCACTGAAGAATTCAGAAAAG
ACGGGGTTCCAATAGGATACAAAGGGAGTACTTTCCACATGGTCATAAAGGGTTTCCTGATTCAGGGTGGAAATTTTGTT
AATGGAGATGGTACAGGAGTTGCCAGCATTTACCAGAGGCCATTTGCAGATGAAAATTTTACACTTAGACTTAGGCTCCA
GGCCTACTTTCTATGGCAAACAGGGGTCCCAGTAAAAATGGCGGTCAGTTCTTTATCTCCTGCTGTAACTGTGATTGGCT
GGATGGGAAGCATGTAGTGTTTCGGCAAAATCATTGATGGACTTCTAGCGATGAGAAAGATTGAGAATGTTCCTATAGGC
CCCAACAAGAAGCCCAAGTTGCCTGTGGTAATCTCAGTGTGGGGAGATGTA

Alignment

ORF - retro_dord_447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.89 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVANSSPVNPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIK
          M.VAN.SP.NP...FDVSI.GQEVG.MKIELFADVV..T.ENFRQFCT.EFRKDGVPIGYKGSTFH.VIK
Retrocopy MMVANVSPINPIMLFDVSISGQEVGHMKIELFADVVLQTTENFRQFCTEEFRKDGVPIGYKGSTFHMVIK

Parental  DFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHS-APGLLSMANSGPSTNGCQFFITCSKCDWLDGKHV
          .F.IQGG.FVNGDGTGVASIY..PFADENF.LR...APGLLSMAN.GPS.NG.QFFI.C..CDWLDGKHV
Retrocopy GFLIQGGNFVNGDGTGVASIYQRPFADENFTLRLR<APGLLSMANRGPSKNGGQFFISCCNCDWLDGKHV

Parental  V-FGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGEM
          V.FGKIIDGLL.MRKIENVP.GPN.KPKLPVVIS..G..
Retrocopy V>FGKIIDGLLAMRKIENVPIGPNKKPKLPVVISVWGDV

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_447 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 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000526	1 retrocopy	retro_amel_1481,
Bos taurus	ENSBTAG00000004590	1 retrocopy	retro_btau_1530,
Callithrix jacchus	ENSCJAG00000003145	5 retrocopies	retro_cjac_129, retro_cjac_1886, retro_cjac_2205, retro_cjac_3120, retro_cjac_4110,
Cavia porcellus	ENSCPOG00000008214	8 retrocopies	retro_cpor_1511, retro_cpor_785, retro_cpor_786, retro_cpor_794, retro_cpor_795, retro_cpor_796, retro_cpor_797, retro_cpor_798,
Dipodomys ordii	ENSDORG00000007389	1 retrocopy	retro_dord_575,
Dipodomys ordii	ENSDORG00000016152	3 retrocopies	retro_dord_151, retro_dord_173, retro_dord_447 ,
Homo sapiens	ENSG00000171960	2 retrocopies	retro_hsap_4740, retro_hsap_928,
Gorilla gorilla	ENSGGOG00000022507	2 retrocopies	retro_ggor_2945, retro_ggor_748,
Macropus eugenii	ENSMEUG00000001691	1 retrocopy	retro_meug_1699,
Myotis lucifugus	ENSMLUG00000025400	2 retrocopies	retro_mluc_1922, retro_mluc_2243,
Macaca mulatta	ENSMMUG00000013129	1 retrocopy	retro_mmul_1124,
Mustela putorius furo	ENSMPUG00000013966	2 retrocopies	retro_mputfur_285, retro_mputfur_542,
Nomascus leucogenys	ENSNLEG00000012313	2 retrocopies	retro_nleu_1242, retro_nleu_289,
Oryctolagus cuniculus	ENSOCUG00000011453	1 retrocopy	retro_ocun_1195,
Procavia capensis	ENSPCAG00000011139	1 retrocopy	retro_pcap_81,
Pongo abelii	ENSPPYG00000001467	2 retrocopies	retro_pabe_3686, retro_pabe_797,
Pan troglodytes	ENSPTRG00000000614	2 retrocopies	retro_ptro_3155, retro_ptro_644,
Pteropus vampyrus	ENSPVAG00000005500	1 retrocopy	retro_pvam_107,
Ictidomys tridecemlineatus	ENSSTOG00000000115	2 retrocopies	retro_itri_1248, retro_itri_412,
Tarsius syrichta	ENSTSYG00000003182	2 retrocopies	retro_tsyr_224, retro_tsyr_647,