RetrogeneDB ID: retro_rnor_736

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:31842998..31843561(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hax1
• Ensembl ID: ENSRNOG00000045647
• Aliases: Hax1, HAX-1, Hs1bp1
• Description: HCLS1-associated protein X-1 [Source:UniProtKB/Swiss-Prot;Acc:Q7TSE9]

Sequence

>retro_rnor_736
ATGAGTGTCTTTGATCTTTTCCAAGGCTTTTTCAGTTTCCCTGAACTTTGGAACCACAGAGATCCTTTCTTTTCTTTCTT
GGGAGGGATGATTCAAGATGATGATAGTGATGATGACAGTGACAACAAAGAGGAGGAAGTCAGAGGCATGTGGGATCCAG
AGAGCTATGCGTTTTATGGTTCTCAGCCTACAAATGAATTCAGTTTCAGTTTCAGCCCTAGAGCAGGGATGTAATTCCAT
GGCAACGTTGGCTTTGATGATCTAGTATGAGATTTTAATAGCATCTTCAGCAACCTGGGGGCCTGTACCTTGCCTTCCCA
CTCTCCTGAACTTCCAGGTCCTGAGTCAGAAAGATCTGGTGAGAGACTATGGAGGGGGCAGACACTTCGAGACTCAATGC
TCAAGTACCCAGATAATCACCAACCCAGGATCTTTGAGGGGGTCTTGAAGACTCATGCAAAACCTGAATCCTCCAAACCA
GCTCTAGATTGGGGGTCCCAGGGACTTTTCACAGGTTAGGCGATACGTGGCCTGTGATTCCCCATTCTGGAGCCAGAGAG
GAC

Alignment

ORF - retro_rnor_736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.13 %
• Parental protein coverage: 99.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVFDLFRGFFGFPGPRSHRDPFF---GGMTRDDD--DDEDDEEEEDSGAWGRESYAFDGFHPTEEFGFS
          MSVFDLF.GFF.FP....HRDPFF...GGM..DDD..DD.D..EEE..G.W..ESYAF.G..PT.EF.FS
Retrocopy MSVFDLFQGFFSFPELWNHRDPFFSFLGGMIQDDDSDDDSDNKEEEVRGMWDPESYAFYGSQPTNEFSFS

Parental  FSPRGGMRFHGNFGFDDLVRDFNSIFSEMGAWTLPSHSPELPGPESETPGVRLREGQTLRDSMLKYPDSH
          FSPR.GM.FHGN.GFDDLV.DFNSIFS..GA.TLPSHSPELPGPESE..G.RL..GQTLRDSMLKYPD.H
Retrocopy FSPRAGM*FHGNVGFDDLV*DFNSIFSNLGACTLPSHSPELPGPESERSGERLWRGQTLRDSMLKYPDNH

Parental  QPRIFEGVLESHAKPESSKPAPDWGSQ-GPFHRLDDTWPVSPHSRARED
          QPRIFEGVL..HAKPESSKPA.DWGSQ.G.FHRL.DTWPV.PHS.ARED
Retrocopy QPRIFEGVLKTHAKPESSKPALDWGSQ<GTFHRLGDTWPVIPHSGARED

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	17.33 RPM
SRP017611_kidney	0.00 RPM	21.91 RPM
SRP017611_liver	0.13 RPM	13.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_736 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_736 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736 ,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,