RetrogeneDB ID: retro_rnor_1262

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:39327286..39327724(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000039080
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ppp1r14b
• Ensembl ID: ENSRNOG00000021151
• Aliases: Ppp1r14b, PHI-1
• Description: Protein phosphatase 1 regulatory subunit 14B [Source:UniProtKB/Swiss-Prot;Acc:Q8K3F3]

Sequence

>retro_rnor_1262
ATGGCGGACAGCGGCCCCGCGGGGGGTGCGGCGTTGGCTGCCCCGGCCCCGGACCGGGTAGTGGCAGCACAGGGCCCCGA
GTCTACTTCCAGAGTCTCCCTGGGGCCGCAGGCGAAGGCCCGGGGGGCACGGATGATGATGGCCCGGTAAAACGGCAAGG
GAAGGTCAATCAAGTACGACCGCAAGGAGCTGCGGAAGCGCCTCAACCTGGAGGAGTGGATTTTAGAACAGCTCACGCGA
CTCTACGACTGCCAGGAGGAGGAGATCCCAGAGCTGGAGATCGATGTGGATGAACTCTTGGACATGGAAAGTGATGATAC
TCGGGCTGCTAGAGTCAAAGAGCTGCTAGTTGACTGTTACAAACCCACTGAGGCCTTCATCTCTGGCCTGCTGGACAAGA
TCCGGGGCATGCAGAAGCTGAGCACACCCTAGAAGAAA

Alignment

ORF - retro_rnor_1262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADSGPAGGAALAAPAP-GPGSGSTGPRVYFQSPPGAAGEGPGGADDDGPVRRQ-GKVTVKYDRKELRKR
          MADSGPAGGAALAAPAP.GPGSGSTGPRVYFQS.PGAAGEGPGG.DDDGPV.RQ.G....KYDRKELRKR
Retrocopy MADSGPAGGAALAAPAP<GPGSGSTGPRVYFQSLPGAAGEGPGGTDDDGPVKRQ>GR-SIKYDRKELRKR

Parental  LNLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDTRAARVKELLVDCYKPTEAFISGLLDKIRGM
          LNLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDTRAARVKELLVDCYKPTEAFISGLLDKIRGM
Retrocopy LNLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDTRAARVKELLVDCYKPTEAFISGLLDKIRGM

Parental  QKLSTPQKK
          QKLSTP.KK
Retrocopy QKLSTP*KK

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	14.02 RPM
SRP017611_kidney	0.07 RPM	17.03 RPM
SRP017611_liver	0.00 RPM	8.54 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1262 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1262 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018019	1 retrocopy	retro_amel_934,
Felis catus	ENSFCAG00000030667	1 retrocopy	retro_fcat_1417,
Mus musculus	ENSMUSG00000056612	5 retrocopies	retro_mmus_1045, retro_mmus_2245, retro_mmus_2624, retro_mmus_30, retro_mmus_3473,
Otolemur garnettii	ENSOGAG00000030926	2 retrocopies	retro_ogar_3158, retro_ogar_376,
Pteropus vampyrus	ENSPVAG00000017120	1 retrocopy	retro_pvam_1095,
Rattus norvegicus	ENSRNOG00000020676	1 retrocopy	retro_rnor_144,
Rattus norvegicus	ENSRNOG00000021151	2 retrocopies	retro_rnor_1262 , retro_rnor_41,