RetrogeneDB ID: retro_rnor_18

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:111995971..111996883(+)
• Located in intron of: ENSRNOG00000000345

Retrocopy information

• Ensembl ID: ENSRNOG00000038337
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Dnajc17
• Ensembl ID: ENSRNOG00000012368
• Aliases: Dnajc17, RGD1308015
• Description: dnaJ homolog subfamily C member 17 [Source:RefSeq peptide;Acc:NP_001178669]

Sequence

>retro_rnor_18
ATGGCGCTGACCAAAGAGTTCTTACAGATGGATCTCTACACGCTGCTGGGCATCGAAGAGAAGGCGACAGACAAAGAGGT
GAAAAAGGCTTATCGACAAAAAGCACTCTCCTGCCACCCAGACAAAAATCCAGATAACCTCAGAGCAGCTGAACTCTTCC
ACCAGCTGTCCCAGGCCTTGGAGGTACTGACTGATGCTGCAGCCAGGACTGCTTATGACAAGGAGAGGAAAGCCAGGAAG
CGGGCCGCAGAGAGGACCCAGAGACTTGACGAGAACAGGAAGAAACTGAAGCTCGATCTGGAGGCCAGGGAGCGGCAGGC
CCAGGCCCAGGGTACTGAGGAAGAGGAGGAGAGCAGGAGCACCACCACACTAGAGCAGAAGATTGCTCGATTACAAGAAG
AGGGTTCCCGTCAGTTGGAAGAGCAGCAAAGGCTGATCCAGGAGCAGACCCGCCAGGACCGAAAACAGAGGCTGAGAGGA
AGAGCAGAAAATAGAGAAGGCAAAAGAACCCCCAAACTAAAGCTTAAGTGGACATGCAAGAAGGAGGACAAGTCCCAAGG
GGGCTACTCCAGAGATGTCCTCCTGAAGCTTTTACATAAGTATGGGGAGGTTCTCAACTTGGTAGTTTCTGGAAGGAAGC
CAGGCAATGCCATAGTGGAGTTTGCAACTGTCAGAGCTGCGGAGCTGGCCGTCAGAAATGAAGTGGGCCTGACTGACAAC
CCTCTGAAGGTTTCCTGGTTGGAGGGACAGCCCCAGGGCACGGTGGACCCCAGTCCCCCAGGACTGACGAAGGGCTCAGT
GTCCTCAGAAAGGGACTATGAGGGTCTGGTCATGATGCGCATGCGCCAGGCCGCTGAACGACAGCAGCTGATGGCCCAGA
TGCAGCAGGAAGATGAGGGGCCGCCCAGGTAG

Alignment

ORF - retro_rnor_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.4 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVTKELLQMDLYALLGIEEKAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLTDAAARA
          MA.TKE.LQMDLY.LLGIEEKA.DKEVKKAYRQKALSCHPDKNPDN.RAAELFHQLSQALEVLTDAAAR.
Retrocopy MALTKEFLQMDLYTLLGIEEKATDKEVKKAYRQKALSCHPDKNPDNLRAAELFHQLSQALEVLTDAAART

Parental  AYDKVRKARKQAAERTQRLDEKRKKVKLDLEARERQAQAQGTEEEEESRSTTTLEQEIARLREEGSRQLE
          AYDK.RKARK.AAERTQRLDE.RKK.KLDLEARERQAQAQGTEEEEESRSTTTLEQ.IARL.EEGSRQLE
Retrocopy AYDKERKARKRAAERTQRLDENRKKLKLDLEARERQAQAQGTEEEEESRSTTTLEQKIARLQEEGSRQLE

Parental  EQQRLIQEQIRQDREQRLRGRTENTEGKGTPKLKLKWKCKKEDESQGGYSRDILLRLLQKYGEVLNLVLS
          EQQRLIQEQ.RQDR.QRLRGR.EN.EGK.TPKLKLKW.CKKED.SQGGYSRD.LL.LL.KYGEVLNLV.S
Retrocopy EQQRLIQEQTRQDRKQRLRGRAENREGKRTPKLKLKWTCKKEDKSQGGYSRDVLLKLLHKYGEVLNLVVS

Parental  KKKAGNAIVEFATVRAAELAVRNEVGLADNPLKVSWLEGQPQGTVDPSPPGLSKGSVLSERDYESLVMMR
          ..K.GNAIVEFATVRAAELAVRNEVGL.DNPLKVSWLEGQPQGTVDPSPPGL.KGSV.SERDYE.LVMMR
Retrocopy GRKPGNAIVEFATVRAAELAVRNEVGLTDNPLKVSWLEGQPQGTVDPSPPGLTKGSVSSERDYEGLVMMR

Parental  MRQAAERQQLIAQMQQEDEGRP
          MRQAAERQQL.AQMQQEDEG.P
Retrocopy MRQAAERQQLMAQMQQEDEGPP

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	4.75 RPM
SRP017611_kidney	0.00 RPM	6.35 RPM
SRP017611_liver	0.00 RPM	3.09 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_18 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_18 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18 , retro_rnor_2319,