RetrogeneDB ID: retro_rnor_2227

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:82566030..82566705(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1561252
• Ensembl ID: ENSRNOG00000009530
• Aliases: Uchl3, RGD1561196
• Description: None

Sequence

>retro_rnor_2227
GAGAGTTAGCACTGGCTGCCGCTGGAGACCAACCCTGAGGTCATCAACCAGTTTCTCAAGCAACTAGGCCTGCATCCTAA
TTGGCAGTTTGTGGATGTGTACGGGCTGGAACCTGAACTTCTCAGCATGGTCCCGAGACGAGTGTGTGCAGTGTTACTCC
TCTTCCCTACTACAGAGAAGTGTGAAGTCTTCAGAACAGAAGAGGAAGCGAAAACGAAATCTCAAGGACAAGATGTTACA
TCATCAGTGTATTTCACCATCAGCAACGCCTGTGGAACCACTGGACTAATCCGTGCCATGGCGAACAACAAGGACAAGAT
GCACTTTGAGTCAGGGTCAACATTGAAAAAGTTCCCGGAGGAGTCTGTGTCAATGATCCCTGAAGAAACAGCCAGATACC
TGAAGAACTAGGACGCCATTCGAGTTACTCATGAAACCAGTGCACAAGAAAGTCAGACTGAGGCACCAAGTATAGATGAA
AAAGTAGATCTTCATTTTATTGCGCTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGACGGAAACCATTTCCAAT
TAACCATGGGAAAACTAGTGATGAGACATTGTTAGAGGATGCCATAGGAGTTTGCAAGAAGTTCATGGACCGTGATCCTG
ATGAGTGCTGTGATGCAATTGCTCTCACAGCAGCA

Alignment

ORF - retro_rnor_2227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.72 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMEPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEE
          E...WLPLE.NPEV.NQFLKQLGLHPNWQFVDVYG.EPELLSMVPR.VCAVLLLFP.TEK.EVFRTEEE.
Retrocopy ES*HWLPLETNPEVINQFLKQLGLHPNWQFVDVYGLEPELLSMVPRRVCAVLLLFPTTEKCEVFRTEEEA

Parental  KIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSALKKFLEESVAMSPEERARHLENY
          K.KSQGQDVTSSVYF...TISNACGT.GLI.A.ANNKDKMHFESGS.LKKF.EESV.M.PEE.AR.L.N.
Retrocopy KTKSQGQDVTSSVYF---TISNACGTTGLIRAMANNKDKMHFESGSTLKKFPEESVSMIPEETARYLKN*

Parental  DAIRVTHETSAHEGQTEAPSIDEKVDLHFIAVVHVDGHLYELDGRKPFPINHGKTSDETLLEDAIEVCKK
          DAIRVTHETSA.E.QTEAPSIDEKVDLHFIA.VHVDGHLYELDGRKPFPINHGKTSDETLLEDAI.VCKK
Retrocopy DAIRVTHETSAQESQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGKTSDETLLEDAIGVCKK

Parental  FMERDPDELRFNAIALSAA
          FM.RDPDE....AIAL.AA
Retrocopy FMDRDPDEC-CDAIALTAA

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2227 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2227 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012261	1 retrocopy	retro_cpor_1217,
Equus caballus	ENSECAG00000024190	1 retrocopy	retro_ecab_400,
Myotis lucifugus	ENSMLUG00000003442	1 retrocopy	retro_mluc_362,
Mus musculus	ENSMUSG00000022111	1 retrocopy	retro_mmus_177,
Oryctolagus cuniculus	ENSOCUG00000006789	1 retrocopy	retro_ocun_382,
Otolemur garnettii	ENSOGAG00000017114	1 retrocopy	retro_ogar_2285,
Rattus norvegicus	ENSRNOG00000009530	1 retrocopy	retro_rnor_2227 ,