RetrogeneDB ID: retro_mmus_368

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:144953520..144954225(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Crlf3
• Ensembl ID: ENSMUSG00000017561
• Aliases: Crlf3, BB164954, Creme9, Cytor4
• Description: cytokine receptor-like factor 3 [Source:MGI Symbol;Acc:MGI:1860086]

Sequence

>retro_mmus_368
GTAAGGTGGATGGGTGATGACTTCACAGTCCAAGATTACAGGCTTCAGTTCCGCAAATGTACTGCAAATCATTTTGAAGA
CATGTATGTAGGTTCTGAAATGGAGTTCATAGTGTTGCACATAGACCCCAATGTGGATTATCAATTCAGAGTCTGCGCCC
AAGGAGACGGCAGGCAGGAATGGACTCCTTGGAGTGTTCCCCAGACAGGGCACTCCACACTGGTGCTTCATGAGTGGACA
ACTGGTTTTGAGGGATACAGTCTGAGCAGTTGAAGGAATATAGCCCTCCGGAATGATGCCGAGTCTTCGGGCGTTCTCGA
CTCCAGCGCTCCATCCTACTTCTGTGGGCAGACGCTGACATTCAGAGTTGAAACTGTGGGGCAGCCAGACTGAAGAGACA
GTACAGGAGTATGTGCAGAAAAGCAGAATGACTACGAATCTCTGCAGCGGGACCAAGCTGTGTGCATCAGCAGGAACCAT
GCAGTCTTTGTCAACGGAAAAGAAATGACCAATCAGTTGCCTGCAGTTACCTCTGGCTCCACTGTCACATTTGACATCAA
AGCTGCGACGCTAGGAACCGCTAACAGCCATGAAGGTGGGAACTCCAAGCTCCGAGTGACCATCAGCTACAGTAACCGGG
AGGTGGTGTTTGACTGGCTGCTCGAGCAGGCCTGTGGCCCTCTTTACTTCAGATGCTCGTTTTTC

Alignment

ORF - retro_mmus_368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.03 %
• Parental protein coverage: 53.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRWCKVDDDFTAQDYRLQFRKCTANHFEDVYVGSETEFIVLHIDPNVDYQFRVCARGDGRQEWSPWSVPQ
          VRW....DDFT.QDYRLQFRKCTANHFED.YVGSE.EFIVLHIDPNVDYQFRVCA.GDGRQEW.PWSVPQ
Retrocopy VRW--MGDDFTVQDYRLQFRKCTANHFEDMYVGSEMEFIVLHIDPNVDYQFRVCAQGDGRQEWTPWSVPQ

Parental  TGHSTLVPHEWTTGFEGYSLSSRRNIALRNDAESSGVLYSSAPTYFCGQTLTFRVETVGQPDRRDSIGVC
          TGHSTLV.HEWTTGFEGYSLSS.RNIALRNDAESSGVL.SSAP.YFCGQTLTFRVETVGQPD.RDS.GVC
Retrocopy TGHSTLVLHEWTTGFEGYSLSS*RNIALRNDAESSGVLDSSAPSYFCGQTLTFRVETVGQPD*RDSTGVC

Parental  AERQNGYESLQRDQAVCISTNGAVFVNGKEMTNQLPAVTSGSTVTFDIEAVTLGTSNSHEGGNAKLRVTI
          AE.QN.YESLQRDQAVCIS.N.AVFVNGKEMTNQLPAVTSGSTVTFDI.A.TLGT.NSHEGGN.KLRVTI
Retrocopy AEKQNDYESLQRDQAVCISRNHAVFVNGKEMTNQLPAVTSGSTVTFDIKAATLGTANSHEGGNSKLRVTI

Parental  SSNNREVVFDWLLEQACGPLYFGCSFF
          S..NREVVFDWLLEQACGPLYF.CSFF
Retrocopy SYSNREVVFDWLLEQACGPLYFRCSFF

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	12.43 RPM
SRP007412_cerebellum	0.00 RPM	20.23 RPM
SRP007412_heart	0.00 RPM	11.67 RPM
SRP007412_kidney	0.00 RPM	13.01 RPM
SRP007412_liver	0.00 RPM	10.57 RPM
SRP007412_testis	0.00 RPM	7.23 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_368 was not detected

EST

No EST(s) were mapped for retro_mmus_368 retrocopy.

TSS

No TSS is located nearby retro_mmus_368 retrocopy 5' end.

Lab

retro_mmus_368 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_368 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014163	1 retrocopy	retro_cjac_1183,
Homo sapiens	ENSG00000176390	3 retrocopies	retro_hsap_2121, retro_hsap_2133, retro_hsap_3360,
Gorilla gorilla	ENSGGOG00000005002	3 retrocopies	retro_ggor_1644, retro_ggor_1649, retro_ggor_2278,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998,
Mus musculus	ENSMUSG00000017561	1 retrocopy	retro_mmus_368 ,
Nomascus leucogenys	ENSNLEG00000005850	4 retrocopies	retro_nleu_1957, retro_nleu_2534, retro_nleu_2899, retro_nleu_2900,
Pongo abelii	ENSPPYG00000008142	3 retrocopies	retro_pabe_1925, retro_pabe_1984, retro_pabe_2672,
Pan troglodytes	ENSPTRG00000008963	2 retrocopies	retro_ptro_1560, retro_ptro_2175,