RetrogeneDB ID: retro_rnor_551

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:270997244..270997534(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cstb
• Ensembl ID: ENSRNOG00000001201
• Aliases: Cstb, Cyb, Epm1, Stfb
• Description: Cystatin-B [Source:UniProtKB/Swiss-Prot;Acc:P01041]

Sequence

>retro_rnor_551
ATGTGTGGCGGGCCATCTGCCACAAAGTCGGACACAGCCGAGACGCAGGAGATCGCCGACAAGGTGAAGTCTGGCTTGAA
GAGAAAGTCAATCAGAAGTTCAATGTCTTTAAAGCCCCGTCCTTCAAGAGACAGGTAGTGGCCGACAGCAACTTCTACAT
CAAGGTTGATGCTGGTCGAGATAAATGTGTACACTTGAGGGTGTTTGAACCCCTCCCTCATGAAAACGAGCCTTTGACGC
CATTTTCTTACCATACCAACAAAGAAAAACACGATGAGCTAACCTGCTTC

Alignment

ORF - retro_rnor_551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.53 %
• Parental protein coverage: 98.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCGAPSATMPATTETQEIADKVKSQL-EEKANQKFDVFKAISFRRQVVAGTNFFIKVDVGEEKCVHLRVF
          MCG.PSAT...T.ETQEIADKVKS.L.EEK.NQKF.VFKA.SF.RQVVA..NF.IKVD.G..KCVHLRVF
Retrocopy MCGGPSATKSDTAETQEIADKVKSGL<EEKVNQKFNVFKAPSFKRQVVADSNFYIKVDAGRDKCVHLRVF

Parental  EPLPHENKPLTLSSYQTDKEKHDELTYF
          EPLPHEN.PLT..SY.T.KEKHDELT.F
Retrocopy EPLPHENEPLTPFSYHTNKEKHDELTCF

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	18.69 RPM
SRP017611_kidney	0.00 RPM	68.18 RPM
SRP017611_liver	0.07 RPM	11.43 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_551 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_551 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000524	1 retrocopy	retro_btau_97,
Loxodonta africana	ENSLAFG00000002664	1 retrocopy	retro_lafr_370,
Myotis lucifugus	ENSMLUG00000022457	1 retrocopy	retro_mluc_379,
Macaca mulatta	ENSMMUG00000012303	1 retrocopy	retro_mmul_1609,
Otolemur garnettii	ENSOGAG00000006101	2 retrocopies	retro_ogar_3274, retro_ogar_3275,
Pteropus vampyrus	ENSPVAG00000007022	1 retrocopy	retro_pvam_1089,
Rattus norvegicus	ENSRNOG00000001201	1 retrocopy	retro_rnor_551 ,
Sarcophilus harrisii	ENSSHAG00000017952	3 retrocopies	retro_shar_229, retro_shar_623, retro_shar_699,