RetrogeneDB ID: retro_rnor_1009

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:72287868..72288330(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000005077
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RGD1563216
• Ensembl ID: ENSRNOG00000012085
• Aliases: Isca2, Hbld1, RGD1563216
• Description: None

Sequence

>retro_rnor_1009
ATGGCGGCCGCCAGGGCCTTGTCCCTAACTGTTGAGGCGTTCGGGGCCCCCATTCCTAGGCGCCAGGGAAGGCTCCTCGC
CGCCTTTCCCAGGCTTTTGACCCGCTGGGAAACAACGTCCTCCATTCCAGAGGCTGGCGAGGGACAGATCCGCCTCACAG
ACAGCTGCGTCCAGAGGCTTCTGGAAATCACCGAAGGGTCAGAATTCCTCAGGCTGCAAGTAGAGGGAGGTGGATGCTCC
GGATTCCAATACAAATTTTCACTGGACACAGTTATTAACCCCGACGACAGGGTATTTGAACAGGGTGGGGCAAGAGTGGT
GGTTGACTCTGATAACTTGGCCTACGTTAAGGGGGCCCAGGTGGACTTCAGCCAAGAACTAATCCGAAGCTCATTCCAGG
TGTTGAATAATCCTCAAGCCCAGCAAGGCTGCTCCTGTGGGTCATCCTTCTCTATCAAAATC

Alignment

ORF - retro_rnor_1009 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAARALSLTAEAFGAAIPRRQGRLLAAFPRLLTRWETTSSIPEAGEGQIRLTDSCVQRLLEITEGSEFL
          MAAARALSLT.EAFGA.IPRRQGRLLAAFPRLLTRWETTSSIPEAGEGQIRLTDSCVQRLLEITEGSEFL
Retrocopy MAAARALSLTVEAFGAPIPRRQGRLLAAFPRLLTRWETTSSIPEAGEGQIRLTDSCVQRLLEITEGSEFL

Parental  RLQVEGGGCSGFQYKFSLDTVINPDDRVFEQGGARVVVDSDSLAYVKGAQVDFSQELIRSSFQVLNNPQA
          RLQVEGGGCSGFQYKFSLDTVINPDDRVFEQGGARVVVDSD.LAYVKGAQVDFSQELIRSSFQVLNNPQA
Retrocopy RLQVEGGGCSGFQYKFSLDTVINPDDRVFEQGGARVVVDSDNLAYVKGAQVDFSQELIRSSFQVLNNPQA

Parental  QQGCSCGSSFSIKI
          QQGCSCGSSFSIKI
Retrocopy QQGCSCGSSFSIKI

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	0.07 RPM	13.30 RPM
SRP017611_kidney	0.00 RPM	25.05 RPM
SRP017611_liver	0.07 RPM	9.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1009 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1009 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1009 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020479	1 retrocopy	retro_cjac_1450,
Dipodomys ordii	ENSDORG00000014857	1 retrocopy	retro_dord_762,
Gorilla gorilla	ENSGGOG00000012894	1 retrocopy	retro_ggor_1610,
Macaca mulatta	ENSMMUG00000006566	1 retrocopy	retro_mmul_643,
Nomascus leucogenys	ENSNLEG00000016268	1 retrocopy	retro_nleu_2754,
Ochotona princeps	ENSOPRG00000011684	2 retrocopies	retro_opri_1068, retro_opri_124,
Pan troglodytes	ENSPTRG00000006536	1 retrocopy	retro_ptro_1504,
Rattus norvegicus	ENSRNOG00000012085	1 retrocopy	retro_rnor_1009 ,