RetrogeneDB ID: retro_rnor_636

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:225846368..225846971(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000016597
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam18b2
• Ensembl ID: ENSRNOG00000050649
• Aliases: Tvp23b, Fam18b2
• Description: None

Sequence

>retro_rnor_636
ATGTTGTCACAGGACAGTAATGACATCACTGAAGATGTCTCACTGTTTGATGCAGAAGAGGAGACAACCAGTAGACCAAG
AAAATCCAAAATCAGACACGCCGTGGCGTCTTTCTTCCGAGTCAGCGCAGTTGTGGTTTATCTCCTCTGCAAGCCGCTCA
GCAGCAGCTTTATTGCCTGCATGGTGACAATTATCCTGCTGCTGTCATGTGACTTTTGGGCAGTGACGAATGTCACTGGT
AGACTAATGGTCAGCCTACGTTGGTGGAATCATATCGACGAGGATGGAAAGAGCCACTGGGTGTTTGAGTCCAGAAAGTC
AACTCCTCAAGACAACAAAACCATTTCTGAGGCCGAGTCAAGAATCTCTTGGTTAGGACTCATCGCCTGCCCAGTCCTGT
GGGTGATCTTTGCCTTTAGTGCCCTTTTTTCCTTCAGAGTGAAGTGGCTGGCTGTGGCGATCATGGGTGTGGTGCTGCAA
GGTGCCAACCTATATGGTTACATCTGGTGTAAACTGGGCAGCAAGAAGAACTTAACCAGCATGGCTACGTCCTATCTTGG
AAAGCAGTTTCTAAGACAAAACGCTGGAGATGGTCAGACTTCA

Alignment

ORF - retro_rnor_636 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSQDSNDDTEDVSLFDAEEETTSRPRKSRIRHPVASFFHLFFRVSAVVVYLLCELLSSSFIACMVTIIL
          MLSQDSND.TEDVSLFDAEEETTSRPRKS.IRH.VAS....FFRVSAVVVYLLC..LSSSFIACMVTIIL
Retrocopy MLSQDSNDITEDVSLFDAEEETTSRPRKSKIRHAVAS----FFRVSAVVVYLLCKPLSSSFIACMVTIIL

Parental  LLSCDFWAVKNVTGRLMVGLRWWNHIDEDGKSHWVFESRKSTPQDSKTISEAESRIFWLGLIACPVLWVI
          LLSCDFWAV.NVTGRLMV.LRWWNHIDEDGKSHWVFESRKSTPQD.KTISEAESRI.WLGLIACPVLWVI
Retrocopy LLSCDFWAVTNVTGRLMVSLRWWNHIDEDGKSHWVFESRKSTPQDNKTISEAESRISWLGLIACPVLWVI

Parental  FAFSALFSFRVKWLAVVIMGVVLQGANLYGYVRCKVGSKKNLTSMATSYLGKQFLRQNAGDGQTS
          FAFSALFSFRVKWLAV.IMGVVLQGANLYGY..CK.GSKKNLTSMATSYLGKQFLRQNAGDGQTS
Retrocopy FAFSALFSFRVKWLAVAIMGVVLQGANLYGYIWCKLGSKKNLTSMATSYLGKQFLRQNAGDGQTS

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	15.31 RPM
SRP017611_kidney	0.14 RPM	52.55 RPM
SRP017611_liver	0.00 RPM	31.60 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_636 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_636 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005330	1 retrocopy	retro_cpor_184,
Dasypus novemcinctus	ENSDNOG00000007609	2 retrocopies	retro_dnov_1041, retro_dnov_1390,
Homo sapiens	ENSG00000171928	1 retrocopy	retro_hsap_2278,
Homo sapiens	ENSG00000175106	1 retrocopy	retro_hsap_1625,
Loxodonta africana	ENSLAFG00000003854	1 retrocopy	retro_lafr_465,
Microcebus murinus	ENSMICG00000015098	4 retrocopies	retro_mmur_1331, retro_mmur_151, retro_mmur_161, retro_mmur_683,
Myotis lucifugus	ENSMLUG00000002825	1 retrocopy	retro_mluc_1484,
Macaca mulatta	ENSMMUG00000019203	5 retrocopies	retro_mmul_1032, retro_mmul_2125, retro_mmul_278, retro_mmul_600, retro_mmul_748,
Nomascus leucogenys	ENSNLEG00000014658	2 retrocopies	retro_nleu_1961, retro_nleu_2008,
Oryctolagus cuniculus	ENSOCUG00000000498	1 retrocopy	retro_ocun_759,
Otolemur garnettii	ENSOGAG00000012225	1 retrocopy	retro_ogar_978,
Pan troglodytes	ENSPTRG00000007790	1 retrocopy	retro_ptro_20,
Pan troglodytes	ENSPTRG00000008796	1 retrocopy	retro_ptro_996,
Rattus norvegicus	ENSRNOG00000050649	1 retrocopy	retro_rnor_636 ,
Ictidomys tridecemlineatus	ENSSTOG00000000642	6 retrocopies	retro_itri_1415, retro_itri_1841, retro_itri_310, retro_itri_473, retro_itri_711, retro_itri_782,
Tarsius syrichta	ENSTSYG00000008082	2 retrocopies	retro_tsyr_2000, retro_tsyr_530,