RetrogeneDB ID: retro_rnor_2853

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:114789561..114789976(+)
• Located in intron of: ENSRNOG00000014789

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cst3
• Ensembl ID: ENSRNOG00000005195
• Aliases: Cst3, CYSC
• Description: Cystatin-C [Source:UniProtKB/Swiss-Prot;Acc:P14841]

Sequence

>retro_rnor_2853
ATGGCCAGCCCGCTGCGCTCCTTGATGCTACTGCTGGCCGTCCTGGCGGTGGCCTGGGCCGGAACCTCCAGGCCACCCCC
GCGATTGTTGGGAGCTCCGCAGGAGGCAGATGCCAGCGAGGAGGGCGTGCAGCGAGCGTTGGACTTCGCAGTAAGCAGTA
CAAGGGCAGCAAAGATGCATACCACAGCCGCGCGCCGTACAGGTGGTGAGAGCTCGTAAGCAGCTTGTGGCTGGAATAAA
CTATTATTTGGATGTGGAGATGGGCCGAACTACATGTACCAAGTCCCAGCCAAATTTGACTAACTGTCCTTTCCACGACC
AGCCCCATCTGATGAGGAAGGCACTCTGCTCCTTCCAGATCTACAGCGTGCCCTGGAAAGGCACACACACCCTGACAAAA
TCCAGCTGCAAAAAT

Alignment

ORF - retro_rnor_2853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.05 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASPLRSLMLLLAVLAVAWAGTSRPP-PRLLGAPQEADASEEGVQRALDFAVSEYNKGSNDAY-HSRAIQ
          MASPLRSLMLLLAVLAVAWAGTSRPP.P...G..........G...........Y...........RA.Q
Retrocopy MASPLRSLMLLLAVLAVAWAGTSRPP<PAIVGSSAGGRCQRGGRAASVGLRSKQYKGSKDAYH<QPRAVQ

Parental  VVRARKQLVAGINYYLDVEMGRTTCTKSQTNLTNCPFHDQPHLMRKALCSFQIYSVPWKGTHTLTKSSCK
          VVRARKQLVAGINYYLDVEMGRTTCTKSQ.NLTNCPFHDQPHLMRKALCSFQIYSVPWKGTHTLTKSSCK
Retrocopy VVRARKQLVAGINYYLDVEMGRTTCTKSQPNLTNCPFHDQPHLMRKALCSFQIYSVPWKGTHTLTKSSCK

Parental  N
          N
Retrocopy N

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	1.37 RPM	664.32 RPM
SRP017611_kidney	0.49 RPM	152.75 RPM
SRP017611_liver	0.67 RPM	35.37 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2853 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2853 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010076	1 retrocopy	retro_amel_935,
Felis catus	ENSFCAG00000024003	1 retrocopy	retro_fcat_1975,
Loxodonta africana	ENSLAFG00000015020	1 retrocopy	retro_lafr_777,
Myotis lucifugus	ENSMLUG00000028312	2 retrocopies	retro_mluc_2081, retro_mluc_2613,
Mustela putorius furo	ENSMPUG00000001122	2 retrocopies	retro_mputfur_716, retro_mputfur_801,
Rattus norvegicus	ENSRNOG00000005195	1 retrocopy	retro_rnor_2853 ,