RetrogeneDB ID: retro_rnor_1689

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:223573751..223574142(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FIS1
• Ensembl ID: ENSRNOG00000001420
• Aliases: Fis1, Ttc11
• Description: Mitochondrial fission 1 protein [Source:UniProtKB/Swiss-Prot;Acc:P84817]

Sequence

>retro_rnor_1689
ATAAAAGCTGTACTGAATGAGCTGGTGTCTGGAGAATCTGGGAAGCTCGAAAGGAAATTTCAGTCTGAGCAGGCAGCCAG
TTCTGTCTTCAAGAACAAACAGTTTGGGTATAAATGGTGCCTGGTGTGAACCGAATACGAGAACAGCATCAGTAGGGCAT
CACATTGCTGGGGGAGCCGTTGCCCAACAGGGGAAGAGGGACACAAATTGTCTTCTACCTGGCAGAGGATAACTACGACA
CAAGGACTATGAAAACACTAAAGCATGTGTGAGGGCTGCTGTAGACTAAACTGCAAACAACCAGGAGAAAGAACTAGAAT
GCCCTGTTGACAAGACCATGAAAATGGACTGGTAAACATGGTTGTTGTTGATAGATGGCCATCATTGTGGA

Alignment

ORF - retro_rnor_1689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.82 %
• Parental protein coverage: 88.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEAVLNELVSVEDLKNFERKFQSEQAAGSVSKSTQFEYAWCLVRSKYNDDIRR-GIVLLEELLPKGSKEE
          ..AVLNELVS.E..K..ERKFQSEQAA.SV.K..QF.Y.WCLV...Y...I.R.GI.LL.E.LP......
Retrocopy IKAVLNELVSGESGK-LERKFQSEQAASSVFKNKQFGYKWCLV*TEYENSISR<GITLLGEPLPNRGRGT

Parental  QRDYVFYLAVGNYRLKEYEKALKYVRGLLQTEPQ-NNQAKELERLIDKAMKKDGLVGMAIVGGMALG
          Q...VFYLA..NY......K.LK.V.GLL.T..Q.NNQ.KELE...DK.MK.D.........G...G
Retrocopy Q--IVFYLAEDNYDTRTM-KTLKHV*GLL*TKLQ<NNQEKELECPVDKTMKMDW*TWLLLIDGHHCG

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	52.48 RPM
SRP017611_kidney	0.00 RPM	43.96 RPM
SRP017611_liver	0.00 RPM	23.94 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1689 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1689 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013800	2 retrocopies	retro_cfam_557, retro_cfam_755,
Callithrix jacchus	ENSCJAG00000016053	1 retrocopy	retro_cjac_1913,
Loxodonta africana	ENSLAFG00000020494	1 retrocopy	retro_lafr_702,
Myotis lucifugus	ENSMLUG00000024207	1 retrocopy	retro_mluc_168,
Monodelphis domestica	ENSMODG00000005034	1 retrocopy	retro_mdom_1773,
Otolemur garnettii	ENSOGAG00000028158	1 retrocopy	retro_ogar_1544,
Rattus norvegicus	ENSRNOG00000001420	2 retrocopies	retro_rnor_1659, retro_rnor_1689 ,
Sus scrofa	ENSSSCG00000027757	1 retrocopy	retro_sscr_1083,