RetrogeneDB ID: retro_rnor_2656

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:129744554..129745268(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pcbp3
• Ensembl ID: ENSRNOG00000001245
• Aliases: None
• Description: poly(rC)-binding protein 3 [Source:RefSeq peptide;Acc:NP_001011945]

Sequence

>retro_rnor_2656
ATGGACACCGGTGTGACTGAAGGTGGATTAAATGTCACTCTCACCATCAGGCTACTTATGCACGGAAAGGAAGTTGGCAG
TATCATCGGAAAGAAAGGAGAATCTGTTAAGAAGATGCGGGAGGAGAGTGGTGCACGTATCAACATCTCAGAAGGGAATT
GTCCTAAGAGAATTATCACTTTGGCTGGACCGACTAATGCCATCTTCAAAGCCTTCGCTATGATCATTGACAAACTGGAA
GAGGACATAAGCAGCTCTATGACCAATAGCACAGCTGCCCGTAGACCCCCGGTTACCTCACGGCTGGTGGTTCCTGCTAG
TTAGTGTGGCTCTCTTATTGGAAAAGGTGGTTGCAAGATCAAGGAAATAAGAGAGAGTACAGGGGCTCAGGTCCAGGTGG
CAGGGGATATGCTCCCCAACTCTACTGAGCGAGCAATCACTATTGCTGGCATTCCGCAATCCATCATTGAGTGTGTCAAA
CAGATCTGCGTGGTCATGTTGGAGTCCCCCCTGAAGGGCGTGACCATCCCGTACCGGCCCAAGCCCTCCAGTTCTCCAGT
CATCTTTGCAGGTGGTCAGGCCTATACCATTCAAGGACAGTATGCCATTCCACAGCCAGATTTGACCAAGCTGCACCAGT
TGGCAATGCAACAGTCTCATTTTCCCATGACCCATGGCAACACCGGATTCAGTGGCATTGAATCCAGCTCTCCA

Alignment

ORF - retro_rnor_2656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.58 %
• Parental protein coverage: 75.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESKVSEGGLNVTLTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGNCPERIVTITGPTDAIFK
          M...V.EGGLNVTLTIRLLMHGKEVGSIIGKKGE.VKKMREESGARINISEGNCP.RI.T..GPT.AIFK
Retrocopy MDTGVTEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPKRIITLAGPTNAIFK

Parental  AFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPN
          AFAMI..K.EEDI..SM.NS.A...PPVT.RLVVPAS.CGSLIGKGG.KIKEIRESTGAQVQVAGDMLPN
Retrocopy AFAMIIDKLEEDISSSMTNSTAARRPPVTSRLVVPAS*CGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN

Parental  STERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPYRPKPASTPVIFAGGQAYTIQGQYAIPHPDQLT
          STERA.TI.G.P..II.CVKQICVVMLESP.KG.TIPYRPKP.S.PVIFAGGQAYTIQGQYAIP.PD.LT
Retrocopy STERAITIAGIPQSIIECVKQICVVMLESPLKGVTIPYRPKPSSSPVIFAGGQAYTIQGQYAIPQPD-LT

Parental  KLHQLAMQQTPFPPLGQTNPAFPGLDASPP
          KLHQLAMQQ..F.P....N..F.G...S.P
Retrocopy KLHQLAMQQSHF-PMTHGNTGFSGIESSSP

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	5.82 RPM	37.89 RPM
SRP017611_kidney	9.84 RPM	6.56 RPM
SRP017611_liver	3.70 RPM	2.29 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2656 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2656 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2656 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003648	1 retrocopy	retro_cpor_257,
Dipodomys ordii	ENSDORG00000003640	2 retrocopies	retro_dord_742, retro_dord_748,
Myotis lucifugus	ENSMLUG00000003074	1 retrocopy	retro_mluc_574,
Nomascus leucogenys	ENSNLEG00000002639	1 retrocopy	retro_nleu_2044,
Oryctolagus cuniculus	ENSOCUG00000002696	1 retrocopy	retro_ocun_1257,
Rattus norvegicus	ENSRNOG00000001245	1 retrocopy	retro_rnor_2656 ,
Rattus norvegicus	ENSRNOG00000036852	2 retrocopies	retro_rnor_1238, retro_rnor_2088,
Sorex araneus	ENSSARG00000007629	1 retrocopy	retro_sara_414,
Tursiops truncatus	ENSTTRG00000015075	1 retrocopy	retro_ttru_1095,