RetrogeneDB ID: retro_rnor_1728

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:25839294..25839670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Xlr4a
• Ensembl ID: ENSRNOG00000017224
• Aliases: Xlr4a, RGD1565442
• Description: Protein Xlr4a; Similar to X-linked lymphocyte regulated gene 4 (Predicted) [Source:UniProtKB/TrEMBL;Acc:D4A7L7]

Sequence

>retro_rnor_1728
CTCCCGCATAAGTGAATACAGGAGATTTATCAGGAATATTATCATCAGTTTTTGATTTGGGTTGTGAAGCTGAATATCGA
TGTAGACCAAATCAAGAAACAGGCTGAAAAACTCTCCAATATACTTGATGAGAAACAGCTTTTGACATAATTTCAAGGTG
TTCATAAACAGGAAGTAGAATAATTTAAGAAGGTATGTGATCGACACTTGGAGAATCTACAGACTATTAAGAGATGTTGC
CAAAAAGTGATGGTTGAGGAAGTCAGGAAACAAGCTGACATCTTAGAGAAGAAACTTACTACGGTAAGTTACTCATTTAA
AGCAACTAGAAGAAGACGCTGGTGTTCAATCATCTCTTCTCTCCCTATTATTCTCC

Alignment

ORF - retro_rnor_1728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.63 %
• Parental protein coverage: 58.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQHEQRQKLYQDYSHQFLTLAVMWNIDVEQVKKHAEKLSNILDEQQKLFQQFQGIHMQKIEEFKELCDRH
          L.H...Q..YQ.Y.HQFL...V..NIDV.Q.KK.AEKLSNILDE.Q.L...FQG.H.Q..E.FK..CDRH
Retrocopy LPHK*IQEIYQEYYHQFLIWVVKLNIDVDQIKKQAEKLSNILDEKQ-LLT*FQGVHKQEVE*FKKVCDRH

Parental  LKNLQAIKRCRRKAIVEEARKQMGCLERKLTEET-VHVKQQEEREGNQSPLLSLLFS
          L.NLQ.IKRC..K..VEE.RKQ...LE.KLT.....H.KQ.EE..G.QS.LLSLLFS
Retrocopy LENLQTIKRCCQKVMVEEVRKQADILEKKLTTVS>THLKQLEEDAGVQSSLLSLLFS

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1728 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1728 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1728 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013389	2 retrocopies	retro_chof_1384, retro_chof_2693,
Callithrix jacchus	ENSCJAG00000001658	1 retrocopy	retro_cjac_2710,
Cavia porcellus	ENSCPOG00000001202	1 retrocopy	retro_cpor_686,
Dasypus novemcinctus	ENSDNOG00000017387	2 retrocopies	retro_dnov_2623, retro_dnov_739,
Dasypus novemcinctus	ENSDNOG00000017624	3 retrocopies	retro_dnov_2294, retro_dnov_2402, retro_dnov_420,
Echinops telfairi	ENSETEG00000007664	1 retrocopy	retro_etel_1510,
Myotis lucifugus	ENSMLUG00000010711	2 retrocopies	retro_mluc_1098, retro_mluc_1839,
Otolemur garnettii	ENSOGAG00000024543	1 retrocopy	retro_ogar_633,
Rattus norvegicus	ENSRNOG00000017224	1 retrocopy	retro_rnor_1728 ,
Ictidomys tridecemlineatus	ENSSTOG00000001853	1 retrocopy	retro_itri_931,