RetrogeneDB ID: retro_mmus_1438

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:16099605..16100109(+)
• Located in intron of: ENSMUSG00000041974

Retrocopy information

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

Parental gene information

• Parental gene symbol: Folr1
• Ensembl ID: ENSMUSG00000001827
• Aliases: Folr1, FBP1, Folbp-1, Folbp1
• Description: folate receptor 1 (adult) [Source:MGI Symbol;Acc:MGI:95568]

Sequence

>retro_mmus_1438
CACTGCGGAACTATGACATTGGAATGCAAAGGGCACTTTATCCAAGACACCTGCCTCTATGAGTGTTCCCAGAACTTGAG
ACCCTGGATACAGTAGGTGGACCAGAACTGGTGCAAAGAGCGGATCCTTGACGTTCCCCTGTGAAAGAGGACTGTCAGCA
GTGGTGGGAGGACTGCCAGAGCTCTTTTACCTGCAAGAGCAACTGGCACAAGGGAAGGAACTGGTCCTCGGAGCATAATG
AGCTTCCTGTGGGAGCCTCCTGCCTTCCCTTCACAGTCTTACTTCCCCACATTTGCTGCTCTGTGTGAGGAAATCTGGAG
CCACTCCTACAAGCTCAGCAACTACAGCAGAGGGAGCAGCTGCTGCATTCAGATGTGGGTAGACCCAGCCCAAGGCAACC
CCAAAGAGGAAGTGGCAAGGTTCTATGCCATTAGTGGAGCTGGGCTTCATGGGGCCTGGCCAATTGTGCGCAGCCTGTCC
TTATTGCTGCTCTGGGTGTTCAGC

Alignment

ORF - retro_mmus_1438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.56 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HCGTMTSECKRHFIQDTCLYECSPNLGPWIQQVDQSWRKERILDVPL-CKEDCQQWWEDCQSSFTCKSNW
          HCGTMT.ECK.HFIQDTCLYECS.NL.PWIQ.VDQ.W.KERILDVPL..KEDCQQWWEDCQSSFTCKSNW
Retrocopy HCGTMTLECKGHFIQDTCLYECSQNLRPWIQ*VDQNWCKERILDVPL<VKEDCQQWWEDCQSSFTCKSNW

Parental  HKGWNWSSGHNECPVGASCHPFTF-YFPTSAALCEEIWSHSYKLSNYSRGSGRCIQMWFDPAQGNPNEEV
          HKG.NWSS.HNE.PVGASC.PFT..YFPT.AALCEEIWSHSYKLSNYSRGS..CIQMW.DPAQGNP.EEV
Retrocopy HKGRNWSSEHNELPVGASCLPFTV>YFPTFAALCEEIWSHSYKLSNYSRGSSCCIQMWVDPAQGNPKEEV

Parental  ARFYAEAMSGAGFHGTWPLLCSLSLVLLWVIS
          ARFY..A.SGAG.HG.WP...SLSL.LLWV.S
Retrocopy ARFY--AISGAGLHGAWPIVRSLSLLLLWVFS

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
SRP007412_brain	0.00 RPM	2.36 RPM
SRP007412_cerebellum	0.00 RPM	4.04 RPM
SRP007412_heart	0.03 RPM	0.22 RPM
SRP007412_kidney	0.04 RPM	206.34 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	0.00 RPM	16.05 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1438 was not detected

EST

No EST(s) were mapped for retro_mmus_1438 retrocopy.

TSS

No TSS is located nearby retro_mmus_1438 retrocopy 5' end.

Lab

retro_mmus_1438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1438 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005777	1 retrocopy	retro_cfam_1723,
Callithrix jacchus	ENSCJAG00000015224	1 retrocopy	retro_cjac_3330,
Dasypus novemcinctus	ENSDNOG00000000856	1 retrocopy	retro_dnov_1751,
Echinops telfairi	ENSETEG00000015365	2 retrocopies	retro_etel_1160, retro_etel_128,
Myotis lucifugus	ENSMLUG00000014126	2 retrocopies	retro_mluc_1199, retro_mluc_567,
Monodelphis domestica	ENSMODG00000008017	1 retrocopy	retro_mdom_990,
Monodelphis domestica	ENSMODG00000008032	1 retrocopy	retro_mdom_588,
Monodelphis domestica	ENSMODG00000008042	1 retrocopy	retro_mdom_648,
Mus musculus	ENSMUSG00000001827	1 retrocopy	retro_mmus_1438 ,
Oryctolagus cuniculus	ENSOCUG00000000165	1 retrocopy	retro_ocun_472,
Otolemur garnettii	ENSOGAG00000000641	5 retrocopies	retro_ogar_2539, retro_ogar_2666, retro_ogar_2758, retro_ogar_2908, retro_ogar_532,
Tarsius syrichta	ENSTSYG00000003503	3 retrocopies	retro_tsyr_1057, retro_tsyr_111, retro_tsyr_1651,