RetrogeneDB ID: retro_rnor_1194

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:51510690..51511224(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Calcoco2
• Ensembl ID: ENSRNOG00000031074
• Aliases: None
• Description: calcium binding and coiled-coil domain 2 [Source:MGI Symbol;Acc:MGI:1343177]

Sequence

>retro_rnor_1194
CTGGACTCCACCATGGAGGAGCGCCATGGCAATTTCTCTCAGGTTCTGTTTAACAATGTGGAGAAGTTCTATATTCCTGG
AGATGTCGTGTGCTGTTACACCCTCACTGAAAAGTTCGTCCCTTGTCCCAAAGACTGGATCGGCATCTTTAAAGTAGGGT
GGGAGATGACCCAGGAGTATTACATCTTCATGTGGGCCCCCTTGCCCGATGACCTAAACACAGAATCAGGGACACAGCAG
AAAATCCAATTCAAAGCTTACTATCTTCCCAAGGATGAAGAGCATTACCAGTTCTGCTATGTGGATGAAGATGGTTTGGT
CCAAGGAATAAGAATCCCCTTCCAGTTCCGTCCAGACTCTGAGGAGGACATAATGATTGTTATCAATAAGGAAAAGATAG
ACAAGATGGAACAGCTCAGGGAGGAGCTTTACCAAGAAAACCAGAAGCTGAAAGACAAGTATGCTGACCTCCATGAGCAG
CTCCAGAGGAAGCAGGTGGCGTTGGAGGCAACACAGAGGATGAATGAGAGCTTA

Alignment

ORF - retro_rnor_1194 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.5 %
• Parental protein coverage: 65.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IDSTMEERHSNFSQVLFNNVEKFYIPGDVVCCYTLTEKFVPRPKDWVGVFKVGWETTQEYYTFMWAPMPD
          .DSTMEERH.NFSQVLFNNVEKFYIPGDVVCCYTLTEKFVP.PKDW.G.FKVGWE.TQEYY.FMWAP.PD
Retrocopy LDSTMEERHGNFSQVLFNNVEKFYIPGDVVCCYTLTEKFVPCPKDWIGIFKVGWEMTQEYYIFMWAPLPD

Parental  DLNTESATQQKIQFKAYYLPKDEEHYQFCYVDEDGLVQGISIPFQFPPPDSEEDIMIVINKEKMDEMEQL
          DLNTES.TQQKIQFKAYYLPKDEEHYQFCYVDEDGLVQGI.IPFQF..PDSEEDIMIVINKEK.D.MEQL
Retrocopy DLNTESGTQQKIQFKAYYLPKDEEHYQFCYVDEDGLVQGIRIPFQF-RPDSEEDIMIVINKEKIDKMEQL

Parental  REELYQENQELKDKYADLHEQLQRKQVALEAHTRMNESL
          REELYQENQ.LKDKYADLHEQLQRKQVALEA..RMNESL
Retrocopy REELYQENQKLKDKYADLHEQLQRKQVALEATQRMNESL

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1194 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1194 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1194 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000006056	3 retrocopies	retro_mmus_1016, retro_mmus_1108, retro_mmus_2097,
Otolemur garnettii	ENSOGAG00000011709	1 retrocopy	retro_ogar_3090,
Rattus norvegicus	ENSRNOG00000031074	1 retrocopy	retro_rnor_1194 ,
Ictidomys tridecemlineatus	ENSSTOG00000013395	1 retrocopy	retro_itri_1120,