RetrogeneDB ID: retro_rnor_1821

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:126024632..126025639(+)
• Located in intron of: ENSRNOG00000022938

Retrocopy information

• Ensembl ID: ENSRNOG00000011715
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mtfr1
• Ensembl ID: ENSRNOG00000021359
• Aliases: Mtfr1, RGD1304936
• Description: Mitochondrial fission regulator 1 [Source:UniProtKB/Swiss-Prot;Acc:G3V9A7]

Sequence

>retro_rnor_1821
ATGCTGGGCTGGATTAAGTGCCTGATGAGGATGTGGTTTCAGCGAGTTGGGGTCAGCATGCAGTCGGTTCTGTGGTCTGG
AAAACCATATGGTTCATCTCGAAGTATTGTAAGGAAAATTGGTACCAACTTATCTCTGATTCAGTGTCCAAGAGTTCAAT
TTCAGCTTACCAGCCATGCAACAGAATGGAGTCCCACGCACCCAGGAGAGGATGTGGTGGCAACTTTTGCTGATGTTGGA
TGGGTAGCCACCGATGAAGGAGAATGCTCAACAAGACTCAGGACAGAAGTCAGGTCCAAGCCTCCTCTTGAGAACAACCC
TCCTTGCTTTGAGAAGCCCCCAAGCAGGGGGCTTACCATTTCCTTACCAAACTCGTCTCAAGACAAGCCTTCCCCAAAGA
CAACACTAGCCAGCGAGGAGGCCTTGCAGAAGATCTCTGCACTTGAGAATGAGCTTGCTGCCCTTAGAGCTCAGATTGCC
AAGATTGTGACCCTGCAGGAGCAACAGAGTCCAAGTGCAGGTTGCTTAGATTCTTCCACACCTGTTATTGTAGCACCACC
ACCGCCGCCACCGCCGCCGCCTCCTCCCCCCCCCCCCCACCATTGGTGCTCCACCCAAGTACATCTGCTCTTGATCTGAT
TAAAGAACGAAGAGAGCAAAGACTCAGTGCTGGAAAGACTCTGGCTAAGGGCCATCCAAAGAAGCTTGACATGCCAAATA
TGCTAGAGATCCTTAAAGACATGAACAGTGTGAAGCTATGGCCAGTCAAGAGGTCAGAGAAAGATGAAAAACCTAGGCCA
GTGGATATTACTGACCCTGCTGCCCTCATAGCAGAGGCTCTGAAAAAGAAGTTTGCATATCGGCATCGACACAATAGCCA
AGGAGAAGCTGAAAGAGGAATTCCAAAGCCAGAGTCAGACGCAACCTCAGAACCAGCCCTGTTTGGCCCACATACATTGA
AGTCTACAGGGAAAATGAAGGCTTTAATTGAAAATGTTTCAGACTCC

Alignment

ORF - retro_rnor_1821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLGWIKCLMRMWFQRVGVSMQSVLWSGKPYGSSRSIVRKIGTNLSLIQCPRVQFQLTSHATEWSPTHPGE
          MLGWIKCLMRMWFQRVGVSMQSVLWSGKPYGSSRSIVRKIGTNLSLIQCPRVQFQLTSHATEWSPTHPGE
Retrocopy MLGWIKCLMRMWFQRVGVSMQSVLWSGKPYGSSRSIVRKIGTNLSLIQCPRVQFQLTSHATEWSPTHPGE

Parental  DVVATFADVGWVATDEGECSTRLRTEVRSKPPLENNPPCFEKPPSRH--ISLPNSSQDKPSPKTTLASEE
          DVVATFADVGWVATDEGECSTRLRTEVRSKPPLENNPPCFEKPPSR...ISLPNSSQDKPSPKTTLASEE
Retrocopy DVVATFADVGWVATDEGECSTRLRTEVRSKPPLENNPPCFEKPPSRGLTISLPNSSQDKPSPKTTLASEE

Parental  ALQKISALENELAALRAQIAKIVTLQEQQSPSAGCLDSSTPVIVVPPPPPPPPPPPPLPPP-PLVLHPST
          ALQKISALENELAALRAQIAKIVTLQEQQSPSAGCLDSSTPVIV..P.......PP......PLVLHPST
Retrocopy ALQKISALENELAALRAQIAKIVTLQEQQSPSAGCLDSSTPVIVA-PXXXXXXXPPXXXXX<PLVLHPST

Parental  SALDLIKERREQRLSAGKTLAKGHPKKLDMPNMLEILKDMNSVKLRPVKRSEKDEKPRPVDITDPAALIA
          SALDLIKERREQRLSAGKTLAKGHPKKLDMPNMLEILKDMNSVKL.PVKRSEKDEKPRPVDITDPAALIA
Retrocopy SALDLIKERREQRLSAGKTLAKGHPKKLDMPNMLEILKDMNSVKLWPVKRSEKDEKPRPVDITDPAALIA

Parental  EALKKKFAYRHRHNSQGEAERGIPKPESDATSEPALFGPHTLKSTGKMKALIENVSDS
          EALKKKFAYRHRHNSQGEAERGIPKPESDATSEPALFGPHTLKSTGKMKALIENVSDS
Retrocopy EALKKKFAYRHRHNSQGEAERGIPKPESDATSEPALFGPHTLKSTGKMKALIENVSDS

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	0.93 RPM
SRP017611_kidney	1.05 RPM	17.65 RPM
SRP017611_liver	1.14 RPM	12.57 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1821 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1821 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1821 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012281	1 retrocopy	retro_amel_1640,
Choloepus hoffmanni	ENSCHOG00000006664	3 retrocopies	retro_chof_1268, retro_chof_2700, retro_chof_483,
Dipodomys ordii	ENSDORG00000016322	1 retrocopy	retro_dord_293,
Homo sapiens	ENSG00000066855	1 retrocopy	retro_hsap_4849,
Macaca mulatta	ENSMMUG00000011263	1 retrocopy	retro_mmul_2590,
Mustela putorius furo	ENSMPUG00000009909	2 retrocopies	retro_mputfur_1244, retro_mputfur_894,
Oryctolagus cuniculus	ENSOCUG00000008165	1 retrocopy	retro_ocun_1594,
Pongo abelii	ENSPPYG00000018631	1 retrocopy	retro_pabe_3769,
Rattus norvegicus	ENSRNOG00000021359	1 retrocopy	retro_rnor_1821 ,
Tarsius syrichta	ENSTSYG00000010102	1 retrocopy	retro_tsyr_1899,