RetrogeneDB ID: retro_rnor_364

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:173081..173912(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000037221
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000043068
• Aliases: Tipin, RGD1564084
• Description: None

Sequence

>retro_rnor_364
ATGTTGGAGCAAGAAGAAAATGGCTTGTTTGAAATACCAGATTATGAACATGTAGAGGATGAAACTTTTCCTCCCTTCCC
ACCTCCGGGCTCTCCAGAGAGAGATCCTGCAGAAGCTGAAGCTGATGAAGGGAGTGGAGCACCTGTTCCTGTTCCGCCAA
AGAGAATAGTTAAAAGGAATATACCCAAGCTAGATGCTACAAGATTGACTTCAGAGAGAGGGCTTCCAGCCTTAAGGCAT
GTATTTGATAAGACAAAATTCAAGGGGAAAGGTCATGAGGCTGAAGACTTGAAAACGCTAATCAGACACATGGAGCACTG
GGCGCATAGGCTATTCCCCAAACTGCAATTTGAAGATTTTATTGACAGAGTTGAAAACCTAGGAAATAAAAAGGAGGTTC
AGACCTGTTTAAAACGAATTCGACTTGATCTGCCTATTGTACATGAAGATTTTGTTAACAATAACGATGAAGTTGAGGAA
ACTAACAGCCTTGATGCAGCTGCCACTGGATTTGATGCCTTTGTGACAAGTTCATCTGACAGCAAGAGGTTTGCTTCTGA
AGCGAGTAGAAACCTAACAGAAGAGCAGCAGCAGAGAATTGAGAGAAATAAACAACTGGCCTTGGAAAGAAGGCAGGCAA
AGCTATTGAGTAATAGCCAGTCCCTAGAAAATGACGTGACAGTTGAAGAGAGCAGTACTGGTGAGAATCAAGAAGAGTCA
AATGGATTGATCTCTGCTGATGGTCCACATGACGTTCCTTCTGCCAGCACACAGGAAGAAGGACAGTTGGAAGCAGAGGA
AACACAGCTGGACCATCCTAACTTAGACTAA

Alignment

ORF - retro_rnor_364 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.27 %
• Parental protein coverage: 86.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSGAPVPVPPKRIVKRNIPKLDATRLTSERGLPALRHVFDKTKFKGKGHEAEDLKTLIRHMEHWAHRLFP
          GSGAPVPVPPKRIVKRNIPKLDATRLTSERGLPALRHVFDKTKFKGKGHEAEDLKTLIRHMEHWAHRLFP
Retrocopy GSGAPVPVPPKRIVKRNIPKLDATRLTSERGLPALRHVFDKTKFKGKGHEAEDLKTLIRHMEHWAHRLFP

Parental  KLQFEDFIDRVENLGNKKEVQTCLKRIRLDLPIVHEDFVNNNDEVEETNSLDAAATGFDAFVTSSSDSKR
          KLQFEDFIDRVENLGNKKEVQTCLKRIRLDLPIVHEDFVNNNDEVEETNSLDAAATGFDAFVTSSSDSKR
Retrocopy KLQFEDFIDRVENLGNKKEVQTCLKRIRLDLPIVHEDFVNNNDEVEETNSLDAAATGFDAFVTSSSDSKR

Parental  FASEASRNLTEEQQQRIEKNKQLALERRQAKLLSNSQSLENEIFLNTNVTVEESSTGENQEESNG
          FASEASRNLTEEQQQRIE.NKQLALERRQAKLLSNSQSLEN........T.E............G
Retrocopy FASEASRNLTEEQQQRIERNKQLALERRQAKLLSNSQSLENDVTVEESSTGENQEESNGLISADG

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	2.44 RPM	0.65 RPM
SRP017611_kidney	2.93 RPM	1.81 RPM
SRP017611_liver	0.61 RPM	0.27 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_364 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_364 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004860	1 retrocopy	retro_chof_223,
Dasypus novemcinctus	ENSDNOG00000003177	3 retrocopies	retro_dnov_1334, retro_dnov_1481, retro_dnov_410,
Homo sapiens	ENSG00000075131	1 retrocopy	retro_hsap_4837,
Gorilla gorilla	ENSGGOG00000000061	3 retrocopies	retro_ggor_1268, retro_ggor_2907, retro_ggor_3016,
Loxodonta africana	ENSLAFG00000026016	1 retrocopy	retro_lafr_1104,
Microcebus murinus	ENSMICG00000004386	2 retrocopies	retro_mmur_155, retro_mmur_255,
Macaca mulatta	ENSMMUG00000003695	1 retrocopy	retro_mmul_1582,
Nomascus leucogenys	ENSNLEG00000012909	1 retrocopy	retro_nleu_1336,
Pan troglodytes	ENSPTRG00000007192	2 retrocopies	retro_ptro_1145, retro_ptro_3220,
Rattus norvegicus	ENSRNOG00000043068	1 retrocopy	retro_rnor_364 ,