RetrogeneDB ID: retro_mmus_489

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:136789184..136789520(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mif
• Ensembl ID: ENSMUSG00000033307
• Aliases: Mif, GIF, Glif
• Description: macrophage migration inhibitory factor [Source:MGI Symbol;Acc:MGI:96982]

Sequence

>retro_mmus_489
ATGCCTATGTTCATCGTGAACACCAATGTTCCCCGCACCTCCGTGCCAGAGGGGTTTCTGTCGGAGCTCACCCAGCAGCT
GGCGCAGGCCACCGGCAAGCCCGCACAGTACATCGCAGTGCACGTGCTCCCGGACCAGCTCATGACTTTTAGAGGCACGA
ACGATCCCTGCGCCCTCTGCAGCCTGCACAGCATCGGTGGTACCCAGAACCGCAACTAAAGCAAGCTGCTGTGCGGCCTG
CTGTCCGATCGCCTGCACATCAGCCCGGACCGGGCCTATATCAGCTATTACGACATGAACGCTGCCAACGTGGGCTGGAA
CGGTTCCACCTTCGCT

Alignment

ORF - retro_mmus_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPMFIVNTNVPRASVPEGFLSELTQQLAQATGKPAQYIAVHVVPDQLMTFSGTNDPCALCSLHSIGKIGG
          MPMFIVNTNVPR.SVPEGFLSELTQQLAQATGKPAQYIAVHV.PDQLMTF.GTNDPCALCSLHSIG...G
Retrocopy MPMFIVNTNVPRTSVPEGFLSELTQQLAQATGKPAQYIAVHVLPDQLMTFRGTNDPCALCSLHSIG---G

Parental  AQNRNYSKLLCGLLSDRLHISPDRVYINYYDMNAANVGWNGSTFA
          .QNRN.SKLLCGLLSDRLHISPDR.YI.YYDMNAANVGWNGSTFA
Retrocopy TQNRN*SKLLCGLLSDRLHISPDRAYISYYDMNAANVGWNGSTFA

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	0.02 RPM	41.24 RPM
SRP007412_cerebellum	0.04 RPM	34.35 RPM
SRP007412_heart	0.00 RPM	28.14 RPM
SRP007412_kidney	0.02 RPM	55.09 RPM
SRP007412_liver	0.03 RPM	39.71 RPM
SRP007412_testis	0.00 RPM	11.89 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_489 was not detected

EST

No EST(s) were mapped for retro_mmus_489 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_69753	200 libraries	371 libraries	434 libraries	58 libraries	9 libraries

The graphical summary, for retro_mmus_489 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_489 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010668	3 retrocopies	retro_cjac_2903, retro_cjac_3132, retro_cjac_357,
Cavia porcellus	ENSCPOG00000013520	1 retrocopy	retro_cpor_879,
Dasypus novemcinctus	ENSDNOG00000014555	1 retrocopy	retro_dnov_36,
Equus caballus	ENSECAG00000012792	1 retrocopy	retro_ecab_1122,
Echinops telfairi	ENSETEG00000012052	3 retrocopies	retro_etel_2001, retro_etel_2046, retro_etel_509,
Mus musculus	ENSMUSG00000033307	8 retrocopies	retro_mmus_1573, retro_mmus_1759, retro_mmus_1878, retro_mmus_2182, retro_mmus_2444, retro_mmus_3016, retro_mmus_3315, retro_mmus_489 ,
Ochotona princeps	ENSOPRG00000012184	1 retrocopy	retro_opri_968,
Rattus norvegicus	ENSRNOG00000006589	6 retrocopies	retro_rnor_137, retro_rnor_1608, retro_rnor_1644, retro_rnor_2263, retro_rnor_31, retro_rnor_361,