RetrogeneDB ID: retro_rnor_620

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:175303676..175304255(-)
• Located in intron of: ENSRNOG00000024789

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmed5
• Ensembl ID: ENSRNOG00000000073
• Aliases: Tmed5, LRRG00120
• Description: Transmembrane emp24 domain-containing protein 5 [Source:UniProtKB/Swiss-Prot;Acc:Q6AXN3]

Sequence

>retro_rnor_620
TTCACCTTCATGCTGGTGGCCGGCTGGAAGGAGTGCTTTTACCAGCCCATGCCCCTGAAGGCGTCATTGGAGATCGAGTA
CCAAGTTTTAGATAGAGGAGAATTAGATAATGATTTCCACCTTGCCTTTCCAGAGGGCAGAACCTTAGTTTTTGAACAAA
GAAAATCAGACGGTGTTCATACTGTAGAGGCTGGAGGTGGAGACTCCATGTTCTGCTTTGATAACACACTGAGCGCCATC
TCTGGGAAGGTCATTTTCTTTCAGTTGATCCTCGATAACACGGGAGAAGCTCAAGGACAAGAAGACTGGAAATAGTATAT
TAGTAACACAGATGTTCTGGAGATGAAACTAGAAGATATCCTGGAATCCATCAACAGCATCAAGTCCAGACTAAGCAAAT
GTGGCCACATAGAGACTCTGCTCAGAGCATTTGAAGCTCGTGATCGAAACATACAAGAAAGCAACTTTCATAGAGTCAAT
TTCTGGTCTGTGGTTAACTTGATGGTCATGGTGGTGGTGTCAGCTATTCAAGTTTATACACTGAAAAGTCTGTTTGAAGA
TAAGAGGAAAAGTAGAACT

Alignment

ORF - retro_rnor_620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.14 %
• Parental protein coverage: 84.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTFTLPAGQKECFYQPMPLKASLEIEYQVLDGGELDIDFHLASPEGRTLVFEQRKSDGVHTVETEDGDYM
          FTF.L.AG.KECFYQPMPLKASLEIEYQVLD.GELD.DFHLA.PEGRTLVFEQRKSDGVHTVE...GD.M
Retrocopy FTFMLVAGWKECFYQPMPLKASLEIEYQVLDRGELDNDFHLAFPEGRTLVFEQRKSDGVHTVEAGGGDSM

Parental  FCFDNTFSTISEKVIFFELILDNMGEEVEGQEDWKKYITNTDVLEMKLEDILESINSIKSRLSKSGHIQT
          FCFDNT.S.IS.KVIFF.LILDN.GE...GQEDWK.YI.NTDVLEMKLEDILESINSIKSRLSK.GHI.T
Retrocopy FCFDNTLSAISGKVIFFQLILDNTGE-AQGQEDWK*YISNTDVLEMKLEDILESINSIKSRLSKCGHIET

Parental  LLRAFEARDRNIQESNFDRVNFWSVVNLMVMVVVSAIQVYTLKSLFEDKRKSRT
          LLRAFEARDRNIQESNF.RVNFWSVVNLMVMVVVSAIQVYTLKSLFEDKRKSRT
Retrocopy LLRAFEARDRNIQESNFHRVNFWSVVNLMVMVVVSAIQVYTLKSLFEDKRKSRT

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	16.90 RPM
SRP017611_kidney	0.00 RPM	32.80 RPM
SRP017611_liver	0.00 RPM	79.21 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_620 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_620 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_620 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012192	1 retrocopy	retro_cpor_254,
Oryctolagus cuniculus	ENSOCUG00000012427	1 retrocopy	retro_ocun_566,
Rattus norvegicus	ENSRNOG00000000073	1 retrocopy	retro_rnor_620 ,
Ictidomys tridecemlineatus	ENSSTOG00000028196	1 retrocopy	retro_itri_155,