RetrogeneDB ID: retro_rnor_1883

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:50579691..50579979(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dynlrb1
• Ensembl ID: ENSRNOG00000025715
• Aliases: Dynlrb1, Dncl2a, km23
• Description: Dynein light chain roadblock-type 1 [Source:UniProtKB/Swiss-Prot;Acc:P62628]

Sequence

>retro_rnor_1883
ATGGCAGAGGTGGAGCAAACACTCAAGAGACTTCAGAGCCAGAAAGGGGTGCAGGGAATCATCGTGGCAAACACAGAAGG
CATTCCCATCAAGAGCACAATGGACAGTCCTACCGTTACACAGTATGACAACCTCATGCACAACTTCGTCTTAAAGGTGT
AGAACACTGTGCGTGAGATTGGCCTCCAGAATGACCTAACCTTCCTTTGAATTTGTACTAAGAAAAATGAAATTATGCTG
GCACCAGAGAAAGACTATTTCCTGACTGTGATTCAGAATCCAACTGAA

Alignment

ORF - retro_rnor_1883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYANLMHNFILKARSTVREIDPQNDLTFLR
          MAEVE.TLKRLQSQKGVQGIIV.NTEGIPIKSTMD.PT.TQY.NLMHNF.LK...TVREI..QNDLTFL.
Retrocopy MAEVEQTLKRLQSQKGVQGIIVANTEGIPIKSTMDSPTVTQYDNLMHNFVLKV*NTVREIGLQNDLTFL*

Parental  IRSKKNEIMVAPDKDYFLIVIQNPTE
          I..KKNEIM.AP.KDYFL.VIQNPTE
Retrocopy ICTKKNEIMLAPEKDYFLTVIQNPTE

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	91.38 RPM
SRP017611_kidney	0.00 RPM	47.17 RPM
SRP017611_liver	0.00 RPM	21.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1883 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018199	10 retrocopies	retro_cjac_1010, retro_cjac_1172, retro_cjac_1274, retro_cjac_1539, retro_cjac_2071, retro_cjac_2902, retro_cjac_3185, retro_cjac_3215, retro_cjac_3260, retro_cjac_882,
Equus caballus	ENSECAG00000008404	2 retrocopies	retro_ecab_102, retro_ecab_553,
Echinops telfairi	ENSETEG00000018637	2 retrocopies	retro_etel_218, retro_etel_699,
Homo sapiens	ENSG00000125971	2 retrocopies	retro_hsap_1946, retro_hsap_948,
Gorilla gorilla	ENSGGOG00000023900	1 retrocopy	retro_ggor_764,
Macaca mulatta	ENSMMUG00000031253	1 retrocopy	retro_mmul_779,
Nomascus leucogenys	ENSNLEG00000010082	2 retrocopies	retro_nleu_1478, retro_nleu_2456,
Oryctolagus cuniculus	ENSOCUG00000021027	2 retrocopies	retro_ocun_351, retro_ocun_745,
Otolemur garnettii	ENSOGAG00000016802	2 retrocopies	retro_ogar_7, retro_ogar_983,
Ochotona princeps	ENSOPRG00000004714	1 retrocopy	retro_opri_888,
Pongo abelii	ENSPPYG00000010937	1 retrocopy	retro_pabe_810,
Pan troglodytes	ENSPTRG00000013416	1 retrocopy	retro_ptro_655,
Rattus norvegicus	ENSRNOG00000025715	1 retrocopy	retro_rnor_1883 ,