RetrogeneDB ID: retro_rnor_2150

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:72304911..72305616(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cnppd1
• Ensembl ID: ENSRNOG00000018325
• Aliases: Cnppd1, RGD735175
• Description: Protein CNPPD1 [Source:UniProtKB/Swiss-Prot;Acc:Q6P7B2]

Sequence

>retro_rnor_2150
CTCTACACTGATCCTCGGGAGATCTTTGAGGTGCTGAGTTGGCTGGAGAGTTGTGTGCCTGAGCAGCAAGGACGGCGGCG
GGGCTGGTACACCTACACAGACCTGTGTGTGCTGCTGGAGCAGCCAATGTGGCAGCTCTCTCTGGGCTCCCTCTGCCAGC
GGCTGGTAAAGCTGTCCTGCCTATTAGCCATGGCATATGTGAGCAGTGTGGCCCTGGCTGTGGCATTCGTGGCTGTAATA
CACTAGTCCTTGGGTCTGTCCTCCAGCCCCTCACCAAGTCCTCCTGAACTCACACTGGTCCCCAAGAACCTCTTGCAGCC
CTGCATACCTGCCCCTGTGCCACAGTGCCTGACTAATGTCTCCAGCTGCCTGGAAGACAGTGTAGAGTTGCCGTCGCTCT
GGGGCAGTCTTCTGGACCCATTGACACCCCCTCTGATGCCTCCTCCAGACCCTCCTGCCCCACCTACTCCTTTCCACAAA
TGCCCCTTTTGCCAGAAGTTCCAGAGAAACCCCCCAAATTGCCGTGCCTGTCACCAGCCTAACCGTACAGTGTCTATTGA
TCCTATCCACCCCTTTTACCATACCCATGGCCTGGCCCCACCCTGGGTCTGGAGCCCAGTGGCCCCTCCATTCCTCCAGC
CCCAGCAGTGTTCTCTTTTTAGTGTCATGAAGCTGGCTCGCCTCACGTCTGTTATTTTCCCAGGC

Alignment

ORF - retro_rnor_2150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.02 %
• Parental protein coverage: 57.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYTDPREIFEVLSWLESCVAEQQGRRRGWYTYTDLCVLLEQPMWQLSLGSLCQRLVKLSCLLAVAYVSSV
          LYTDPREIFEVLSWLESCV.EQQGRRRGWYTYTDLCVLLEQPMWQLSLGSLCQRLVKLSCLLA.AYVSSV
Retrocopy LYTDPREIFEVLSWLESCVPEQQGRRRGWYTYTDLCVLLEQPMWQLSLGSLCQRLVKLSCLLAMAYVSSV

Parental  ALAVASMAVIHQSLGLSSSPSPSPPELTLVPKNLLQPCIPAPVPQCLTNVSSCLEDSVELPSLWGSLLDP
          ALAVA..AVIH.SLGLSSSPSPSPPELTLVPKNLLQPCIPAPVPQCLTNVSSCLEDSVELPSLWGSLLDP
Retrocopy ALAVAFVAVIH*SLGLSSSPSPSPPELTLVPKNLLQPCIPAPVPQCLTNVSSCLEDSVELPSLWGSLLDP

Parental  LTPPLMPPPDPPAPPTPFHKCPFCQKFQRNPPNCRACHQPNRTVSIGPIHPFYHTHGLAPPWLWSPVAPP
          LTPPLMPPPDPPAPPTPFHKCPFCQKFQRNPPNCRACHQPNRTVSI.PIHPFYHTHGLAPPW.WSPVAPP
Retrocopy LTPPLMPPPDPPAPPTPFHKCPFCQKFQRNPPNCRACHQPNRTVSIDPIHPFYHTHGLAPPWVWSPVAPP

Parental  FLQPQQCSLFSVMKLARLTSVIFPG
          FLQPQQCSLFSVMKLARLTSVIFPG
Retrocopy FLQPQQCSLFSVMKLARLTSVIFPG

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	0.72 RPM	27.46 RPM
SRP017611_kidney	2.79 RPM	56.52 RPM
SRP017611_liver	2.08 RPM	28.91 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2150 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2150 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000015328	1 retrocopy	retro_mdom_538,
Pteropus vampyrus	ENSPVAG00000010786	1 retrocopy	retro_pvam_857,
Rattus norvegicus	ENSRNOG00000018325	1 retrocopy	retro_rnor_2150 ,