RetrogeneDB ID: retro_dord_399

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_16476:269..1050(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lpcat2
• Ensembl ID: ENSDORG00000013193
• Aliases: None
• Description: lysophosphatidylcholine acyltransferase 2 [Source:MGI Symbol;Acc:MGI:3606214]

Sequence

>retro_dord_399
CTGCAGGCGTGCGTGCTCACCTGAGCCAACCTCACCCGCGTGGAGGTGAGTTCATGCCCGTGCACGTGCCCAGCGCGGAG
GAGAGGAGGGATCCCCTGCTCTCGCCAACGCCGTCCGCGTCAAGATGGCCAACGCCCTGGGGGTCCCCGTGACGGACCAC
ACGTTCGAGGACTGCCGGCTGATGATCTCGGCGGGGGCCCTGCGGCTCCCCATGGAGGCGGGCCTGGTGGAGTTCACCAA
GATCAGTCGGAAACTGCAGCTGGACTGGGACGACATCCACAAGCACCTGGACAAGTTCGCCGCCATCGCTGTGGCCTCCA
AGGGCGGGAAGATCGGCATCGAAGAGTTCTCCAATTACTTGAAACTGCCCGTGACCGAGCCCTTGAGACAGCTCTTCGCC
TTCTTTGACCGGAACCACGACGGCACCATCGACTTCCGGGAGTACGTGATCGGGCTGACGGTCCTGTGCAACCCCGACGA
CACCGAAAAGATCCTGGAGGTGTCCTTCCGGCTCTTCGACCTCGACGCCGACGGCTTCATCACCGAGCAGGAGTTCACCG
CTATCCTCCGCGCGGCCTTTGGAGTGCCGGATCTGGATGTTTCCAGACTCTTCTGGGAAATGGCTGGGAAGAGCTCGGCA
CACATTTCCTTCAAGAGCTTCCGGAAATTTGCCCTCAAGCACCCGGCCTATGCCAAGTTATTTCATTCATACTTAGATCT
CCAGGCGGCCTATATCTATTCCTTACCGCCAGAGATCCAGCCCACTTCGCTGCATTCAAAT

Alignment

ORF - retro_dord_399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.42 %
• Parental protein coverage: 52.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LQLCVLTFCQPFTKVEV-EFMPVQVPNDEEKKDPVL-FASRVRSLMADTLGVPVTDHTYEDCRLMISAGQ
          LQ.CVLT.....T.VEV.EFMPV.VP..EE..DP.L..A..VR..MA..LGVPVTDHT.EDCRLMISAG.
Retrocopy LQACVLT*AN-LTRVEV<EFMPVHVPSAEERRDPLL<LANAVRVKMANALGVPVTDHTFEDCRLMISAGA

Parental  LTLPMEAGLVEFTKISRKLKLDWDGIRKHLDEYASIASSSKGGRIGIEEFAEYLKLPVSDVLRQLFALFD
          L.LPMEAGLVEFTKISRKL.LDWD.I.KHLD..A.IA..SKGG.IGIEEF..YLKLPV...LRQLFA.FD
Retrocopy LRLPMEAGLVEFTKISRKLQLDWDDIHKHLDKFAAIAVASKGGKIGIEEFSNYLKLPVTEPLRQLFAFFD

Parental  RNNDGSIDFREYVIGLAVLCNPANTEEIIQMAFKLFDVDEDGYIMEEEFTTLLQASLGVPDLDVSGLFKE
          RN.DG.IDFREYVIGL.VLCNP..TE.I....F.LFD.D.DG.I.E.EFT..L.A..GVPDLDVS.LF.E
Retrocopy RNHDGTIDFREYVIGLTVLCNPDDTEKILEVSFRLFDLDADGFITEQEFTAILRAAFGVPDLDVSRLFWE

Parental  IAQGDS--ISYEEFKSFALKHPEYAKIFTTYLDLQTCHVFSLPNEAQPAPSIPSN
          .A...S..IS...F..FALKHP.YAK.F..YLDLQ.....SLP.E.QP..S..SN
Retrocopy MAGKSSAHISFKSFRKFALKHPAYAKLFHSYLDLQAAYIYSLPPEIQPT-SLHSN

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_399 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019272	1 retrocopy	retro_btau_64,
Callithrix jacchus	ENSCJAG00000012902	1 retrocopy	retro_cjac_2945,
Dasypus novemcinctus	ENSDNOG00000006859	1 retrocopy	retro_dnov_1735,
Dipodomys ordii	ENSDORG00000013193	1 retrocopy	retro_dord_399 ,
Equus caballus	ENSECAG00000009649	1 retrocopy	retro_ecab_865,
Erinaceus europaeus	ENSEEUG00000014277	1 retrocopy	retro_eeur_109,
Homo sapiens	ENSG00000087253	1 retrocopy	retro_hsap_185,
Gorilla gorilla	ENSGGOG00000005144	1 retrocopy	retro_ggor_266,
Loxodonta africana	ENSLAFG00000003965	1 retrocopy	retro_lafr_66,
Myotis lucifugus	ENSMLUG00000004008	1 retrocopy	retro_mluc_88,
Macaca mulatta	ENSMMUG00000004478	1 retrocopy	retro_mmul_392,
Mus musculus	ENSMUSG00000033192	1 retrocopy	retro_mmus_270,
Nomascus leucogenys	ENSNLEG00000001258	1 retrocopy	retro_nleu_994,
Pongo abelii	ENSPPYG00000007358	1 retrocopy	retro_pabe_445,
Pan troglodytes	ENSPTRG00000008124	2 retrocopies	retro_ptro_171, retro_ptro_2928,
Pteropus vampyrus	ENSPVAG00000007801	1 retrocopy	retro_pvam_173,
Rattus norvegicus	ENSRNOG00000016643	1 retrocopy	retro_rnor_309,
Sorex araneus	ENSSARG00000011914	1 retrocopy	retro_sara_88,
Sarcophilus harrisii	ENSSHAG00000012383	1 retrocopy	retro_shar_116,
Tursiops truncatus	ENSTTRG00000001182	1 retrocopy	retro_ttru_188,