RetrogeneDB ID: retro_rnor_1025

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:99238845..99239232(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000030181
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Carhsp1
• Ensembl ID: ENSRNOG00000002610
• Aliases: Carhsp1, Crhsp-24, Crhsp24
• Description: Calcium-regulated heat stable protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9WU49]

Sequence

>retro_rnor_1025
ATGTCATCTGAGTCTCCTTCGCTGCCACCATAGCCCCCACACATGAGACTTCTGTAGGGCTATTGGATACCCCTTGTGCC
CAGCATTGTTCTCCATCCACGATGAAGGGCAATGTGGTCCCTAGCCCTCTGCCTACATGCCAGACACTTCTCAGTGATGG
TGCAGGCTTTGCAGTGCCCTGTCTACAAGGGAGACTGTAAATGCTTCTGCCGTTCCAAGGGTCATGGCTTCATCATCCTT
GGTGATGGTGGTCCTGACATCTTCTTGCACATCTCTGATGTGGAAGGGGAGTATGTTCCGGTGGAAGGTGATGAGGTCAT
CTATGAGGTGTGCTCTATCCTGCCCAAGAATGAGAAACTCACCCACCTGGCACCAGGGACCACACAT

Alignment

ORF - retro_rnor_1025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.67 %
• Parental protein coverage: 88.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSEPPP-PPQPP-THQTSIGLLDTPRARDRSPSPLRGNVVPSPLPTRRTRT-FSATVRASQGPVYKGVC
          MSSE.P..PP.PP.TH.TS.GLLDTP.A...SPS...GNVV..P.P.....T.FS..V.A.Q.PVYKG.C
Retrocopy MSSESPSLPP*PP<THETSVGLLDTPCAQHCSPSTMKGNVV--PSPLPTCQT>FSVMVQALQCPVYKGDC

Parental  KCFCRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITH
          KCFCRSKGHGFI...DGGPDIFLHISDVEGEYVPVEGDEV.Y..CSI.PKNEKL.......TH
Retrocopy KCFCRSKGHGFIILGDGGPDIFLHISDVEGEYVPVEGDEVIYEVCSILPKNEKLTHLAPGTTH

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	32.50 RPM
SRP017611_kidney	0.00 RPM	57.85 RPM
SRP017611_liver	0.00 RPM	134.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1025 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1025 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1025 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017286	1 retrocopy	retro_cjac_194,
Macropus eugenii	ENSMEUG00000016403	1 retrocopy	retro_meug_1949,
Monodelphis domestica	ENSMODG00000005721	1 retrocopy	retro_mdom_12,
Mus musculus	ENSMUSG00000008393	1 retrocopy	retro_mmus_88,
Rattus norvegicus	ENSRNOG00000002610	1 retrocopy	retro_rnor_1025 ,