RetrogeneDB ID: retro_rnor_2655

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:129361366..129361678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atpif1
• Ensembl ID: ENSRNOG00000013300
• Aliases: Atpif1, Atpi, IF1PA
• Description: ATPase inhibitor, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q03344]

Sequence

>retro_rnor_2655
GGCTCCGCGTGGGCGGCTCGGGCTCAGCTCGGTGTCTGCGGTATTTGGGTCCTACAAACCCTAGGCTTCGTCTCAGATTC
GTTGGAGAGCACAGATGCGGGTGCTGGCTCCATCTGAGAAGCTGGTGGGGCCTTAGGAAAACCAGAGAAGGCTGAAGAGG
ATCGGTACCTCCGAGAGAAGACTAGAAAACAGCCGGCTGTCCTGAAGAAGCACCATGAAGATGAGATTGACCACCATTCG
AAGGAGATAGAGCATCTGCAGAAACAAATTAAACTGCATAAGAAGGTTAAACACCTGAAGAGTAGTGATCAT

Alignment

ORF - retro_rnor_2655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.24 %
• Parental protein coverage: 98.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSALAVRARLGVWGMRVLQTRGFGSDSSESMDSGAGSIREAGGAFGKREKAEEDRYFREKTREQLAALKK
          GSA.A.RA.LGV.G..VLQT.GF.SDS.ES.D.GAGSI.EAGGA.GK.EKAEEDRY.REKTR.Q.A.LKK
Retrocopy GSAWAARAQLGVCGIWVLQTLGFVSDSLESTDAGAGSI*EAGGALGKPEKAEEDRYLREKTRKQPAVLKK

Parental  HHEDEIDHHSKEIERLQKQIERHKKKIKYLKNSEH
          HHEDEIDHHSKEIE.LQKQI..H.KK.K.LK.S.H
Retrocopy HHEDEIDHHSKEIEHLQKQIKLH-KKVKHLKSSDH

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	0.00 RPM	48.24 RPM
SRP017611_kidney	0.00 RPM	56.04 RPM
SRP017611_liver	0.00 RPM	7.19 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2655 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2655 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032458	2 retrocopies	retro_cfam_1777, retro_cfam_651,
Callithrix jacchus	ENSCJAG00000009581	1 retrocopy	retro_cjac_1406,
Dasypus novemcinctus	ENSDNOG00000015460	1 retrocopy	retro_dnov_2592,
Myotis lucifugus	ENSMLUG00000000170	1 retrocopy	retro_mluc_363,
Monodelphis domestica	ENSMODG00000010826	1 retrocopy	retro_mdom_902,
Mustela putorius furo	ENSMPUG00000015536	1 retrocopy	retro_mputfur_1570,
Mus musculus	ENSMUSG00000054428	2 retrocopies	retro_mmus_2516, retro_mmus_908,
Otolemur garnettii	ENSOGAG00000010337	2 retrocopies	retro_ogar_116, retro_ogar_268,
Pteropus vampyrus	ENSPVAG00000017615	1 retrocopy	retro_pvam_817,
Rattus norvegicus	ENSRNOG00000013300	1 retrocopy	retro_rnor_2655 ,
Sorex araneus	ENSSARG00000010860	1 retrocopy	retro_sara_458,
Ictidomys tridecemlineatus	ENSSTOG00000020766	1 retrocopy	retro_itri_1240,