RetrogeneDB ID: retro_rnor_2541

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:140349163..140349787(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Crip2
• Ensembl ID: ENSRNOG00000005041
• Aliases: Crip2, CRP2
• Description: Cysteine-rich protein 2 [Source:UniProtKB/Swiss-Prot;Acc:P36201]

Sequence

>retro_rnor_2541
ATGGCCTCCAAGTGTCCAAGTGTGACAAGACTGTGTACTTCGCCGAGAAGGCAAGCTCTCTGGGCAAGGACTGGCACAAA
TTCTGCCTCAAGTGTGAGCGCTGCAACAAGACACTGACACCCGGCGGCCCTGCTGAGCATGATGGGAAACCATTCTGCCA
CAAGACCTGTTATGCCACACTATTTGGACCCAAAGGCGTGAATACCGGGGGTGCTGGTTCCTAATCTACGAGAAGCGTCC
AACGGAAGCCCCTCAGGTCACTGGCCCCATCGAGGTCCCTGTGGTGCGAACTGAAGAGTGGAAGACCAACGGGTCCCCCA
AGAGTCGCAGCAAAGCCTCTAGTGTCACCACATTCACTGGGGAGCCCAATATGTGTCCTCGAGATGCAACAAGAGAGTGT
ACTTTGCTGAGAAGGTGACCTCCCTGGGCAAGGACTGGCACCAGCCCTGCCTGTGCTGTGAGCGCTGCTCCAAGACACTG
ACCCCAGGCGGGCATGCTGGGCATGCTGGCCAACCCTAATGCCACAAGTCTTGCTATGGAATACTCTTTGGACCCAAAGG
AGTGAAAACTGGTGCTGTGGGCAGCTATATCTATGACAAGGACCTGGAAGGCACAGTTCAGCCT

Alignment

ORF - retro_rnor_2541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MASKCP-KCDKTVYFAEKVSSLGKDWHKFCLKCERCNKTLTPGGHAEHDGKPFCHKPCYATLFGPKGVNI
          MASKCP.KCDKTVYFAEK.SSLGKDWHKFCLKCERCNKTLTPGG.AEHDGKPFCHK.CYATLFGPKGVN.
Retrocopy MASKCP<KCDKTVYFAEKASSLGKDWHKFCLKCERCNKTLTPGGPAEHDGKPFCHKTCYATLFGPKGVNT

Parental  GGAGS-YIYEKPPTEAPQVTGPIEVPVVRTEERKTSG-PPKGPSKASSVTTFTGEP-NMCPRCNKRVYFA
          GGAGS..IYEK.PTEAPQVTGPIEVPVVRTEE.KT.G.PP....K........G.P.....RCNKRVYFA
Retrocopy GGAGS<LIYEKRPTEAPQVTGPIEVPVVRTEEWKTNG>PPRVAAKPLVSPHSLGSP>YVSSRCNKRVYFA

Parental  EKVTSLGKDWHRPCLRCERCSKTLTPGGHAEHDGQPYCHKPCYGILFGPKGVNTGAVGSYIYDKDPEGTV
          EKVTSLGKDWH.PCL.CERCSKTLTPG.......QP.CHK.CYGILFGPKGV.TGAVGSYIYDKD.EGTV
Retrocopy EKVTSLGKDWHQPCLCCERCSKTLTPGXXXXXXXQP*CHKSCYGILFGPKGVKTGAVGSYIYDKDLEGTV

Parental  QP
          QP
Retrocopy QP

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	93.18 RPM
SRP017611_kidney	0.00 RPM	47.66 RPM
SRP017611_liver	0.00 RPM	103.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2541 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000010504	1 retrocopy	retro_meug_481,
Pteropus vampyrus	ENSPVAG00000014236	1 retrocopy	retro_pvam_878,
Rattus norvegicus	ENSRNOG00000003772	1 retrocopy	retro_rnor_1763,
Rattus norvegicus	ENSRNOG00000005041	2 retrocopies	retro_rnor_141, retro_rnor_2541 ,
Rattus norvegicus	ENSRNOG00000027990	2 retrocopies	retro_rnor_2590, retro_rnor_2599,