RetrogeneDB ID: retro_rnor_1608

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:49000806..49001146(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mif
• Ensembl ID: ENSRNOG00000006589
• Aliases: None
• Description: Macrophage migration inhibitory factor [Source:UniProtKB/Swiss-Prot;Acc:P30904]

Sequence

>retro_rnor_1608
ATGCCTATGTTCATCATGAGCACCAATGTTCCTGCTCCTCCCTGCCAGAGGAGTTTCTCTTGGAGCTCACCCAACAGCTG
GCGCAGGCCACTGGCAAGCCGACACAGTACATCACAGTGCATGTGGTCCGGAACCAGCTCATGACTTTTAGCGGCATGAG
CGACCCCGGCACCTCTGTAGCCTGCACAGCACCCGCAAGGTCGGTGGTGCCCAAAACGGCAACTATAGCAAGCTGCTGTG
TGGCTTGCTGTTGGATCTCCTGCACATCAGCCCAGACCGGGTCTACATCAACTATTACGACATGAATGCAGCCAACGTGG
GCTGGAACGGTTCCACCTAC

Alignment

ORF - retro_rnor_1608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.17 %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPMFIVNTNVPR-ASVPEGFLSELTQQLAQATGKPAQYIAVHVVPDQLMTFSGTSDPCA-LCSLHSIGKI
          MPMFI..TNVP...S.PE.FL.ELTQQLAQATGKP.QYI.VHVV..QLMTFSG.SDP...LCSLHS..K.
Retrocopy MPMFIMSTNVPA<SSLPEEFLLELTQQLAQATGKPTQYITVHVVRNQLMTFSGMSDPGT<LCSLHSTRKV

Parental  GGAQNRNYSKLLCGLLSDRLHISPDRVYINYYDMNAANVGWNGSTF
          GGAQN.NYSKLLCGLL.D.LHISPDRVYINYYDMNAANVGWNGST.
Retrocopy GGAQNGNYSKLLCGLLLDLLHISPDRVYINYYDMNAANVGWNGSTY

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	0.07 RPM	82.75 RPM
SRP017611_kidney	0.00 RPM	176.48 RPM
SRP017611_liver	0.00 RPM	125.80 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1608 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1608 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1608 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,