RetrogeneDB ID: retro_rnor_651

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:249646051..249646642(-)
• Located in intron of: ENSRNOG00000015232

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam122b
• Ensembl ID: ENSRNOG00000050146
• Aliases: None
• Description: protein FAM122B [Source:RefSeq peptide;Acc:NP_001160058]

Sequence

>retro_rnor_651
GAGGAGGGCATGGACCTGATCAACCGAGAGACGGTCCACGAGCGCGAGGTGCAGACCGCAATGCAGATAAGCCACTCCTG
GGAGGAAAGTTTCAGCCTGAGTGACAACGACGTGGAGAAATCCGCCTCTCCAAAGCGCATCGATTTCATTCCGGTGTCTC
CAGCACCGTCACCCACCCGGGGAATTGGGAAGCAGTGTTTTTCACCGTCCTTGCAAAGTTTTGTGAGTAGCAACGGATTG
CCTCCAAGTCCTATTCCCAGCCCAACCACCCGGTTTACTACCCGGAGAAGCCAGAGTCCCATCAACTGCATTAGACCAAG
TGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGATTATCAGCCAAAGAGATTTTTCCAGGGCATCACCAACA
TGCTTTCTTCTGACGTTGCACAGCTGTCAGAGCCCGGAGTGTGTGTATCTTCTGATACCCTGGATGGAAACAGCAGCAGT
GCCGGATCTTCCTGTAATTCACCAGCGAAAGTCAGCACTACCACCGACTCTCCTGTGTCGCCTGCCCAAGCAGCCTCCCC
CTTTATTCCAGTAGATGAACTTTCCTCAAAG

Alignment

ORF - retro_rnor_651 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 76.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEGLDLMNRETANEREPQGGMQISHSWDESLSLSDSDFDKPEKLYSPKRIDFTPVSPAPSPTRGFGK-CT
          EEG.DL.NRET..ERE.Q..MQISHSW.ES.SLSD.D....EK..SPKRIDF.PVSPAPSPTRG.GK.C.
Retrocopy EEGMDLINRETVHEREVQTAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSPTRGIGKQCF

Parental  SPSLQMFVGSSEVPPSSVPNP--RHFSRRSQSPVKCIRPSVLGPLKRKGEMEIESQPKRPFQGATNMLST
          SPSLQ.FV.S...PPS..P.P..R...RRSQSP..CIRPSVLGPLKRK.EME...QPKR.FQG.TNMLS.
Retrocopy SPSLQSFVSSNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETDYQPKRFFQGITNMLSS

Parental  DATQLSDFSSC--SDILDGSSVSSGLSSDSLATGSAPAESPVACSNPCSSFILMDDLSPK
          D..QLS....C..SD.LDG.S.S.G.S..S.A..S....SPV......S.FI..D.LS.K
Retrocopy DVAQLSEPGVCVSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQAASPFIPVDELSSK

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	7.84 RPM	0.00 RPM
SRP017611_kidney	8.93 RPM	0.00 RPM
SRP017611_liver	3.36 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_651 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_651 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_651 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_35
Mus musculus	retro_mmus_22
Oryctolagus cuniculus	retro_ocun_205
Bos taurus	retro_btau_103
Canis familiaris	retro_cfam_181
Equus caballus	retro_ecab_91

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001311	1 retrocopy	retro_amel_105,
Bos taurus	ENSBTAG00000001886	1 retrocopy	retro_btau_103,
Canis familiaris	ENSCAFG00000018882	1 retrocopy	retro_cfam_181,
Callithrix jacchus	ENSCJAG00000004313	1 retrocopy	retro_cjac_594,
Cavia porcellus	ENSCPOG00000011218	1 retrocopy	retro_cpor_80,
Equus caballus	ENSECAG00000018643	1 retrocopy	retro_ecab_91,
Felis catus	ENSFCAG00000024842	1 retrocopy	retro_fcat_1575,
Myotis lucifugus	ENSMLUG00000007988	1 retrocopy	retro_mluc_382,
Macaca mulatta	ENSMMUG00000016948	1 retrocopy	retro_mmul_185,
Mustela putorius furo	ENSMPUG00000012690	1 retrocopy	retro_mputfur_64,
Mus musculus	ENSMUSG00000036022	1 retrocopy	retro_mmus_22,
Rattus norvegicus	ENSRNOG00000050146	1 retrocopy	retro_rnor_651 ,
Sus scrofa	ENSSSCG00000012685	1 retrocopy	retro_sscr_60,
Ictidomys tridecemlineatus	ENSSTOG00000006261	1 retrocopy	retro_itri_61,