RetrogeneDB ID: retro_rnor_2199

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:19778718..19779011(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fabp3
• Ensembl ID: ENSRNOG00000012879
• Aliases: None
• Description: Fatty acid-binding protein, heart [Source:UniProtKB/Swiss-Prot;Acc:P07483]

Sequence

>retro_rnor_2199
ACCTGGAAGCCTGTGGACAGCAAGAATTTTGATGGCTACGTGAAGTCATTGGTGTGGGTTTTGCCAATAGGCCGATGACT
CACATAACCAAGCCTACCACAGTCATTGAGAAGAATGGGAATGCTATCACCATAAAGACACACAGTGCCTTCAAGAACGC
AGAGATCGATTTTCAGCTAGGAGTAGATTTCAAAGAGGTAACCGCAGATGTCAGGAAGGTCAAGTCAGTTGTGACACTGG
ACAGAGGCAAACTAGTCCACGTGCAGAAATGGAACAGGCAGGAGACTATGCTT

Alignment

ORF - retro_rnor_2199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.77 %
• Parental protein coverage: 73.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TWKLVDSKNFDDYMKSL-GVGFATRQVASMTKPTTIIEKNGDTITIKTHSTFKNTEISFQLGVEFDEVTA
          TWK.VDSKNFD.Y.KSL.GVGFA.R.....TKPTT.IEKNG..ITIKTHS.FKN.EI.FQLGV.F.EVTA
Retrocopy TWKPVDSKNFDGYVKSL<GVGFANRPMTHITKPTTVIEKNGNAITIKTHSAFKNAEIDFQLGVDFKEVTA

Parental  DDRKVKSVVTLDGGKLVHVQKWDGQETTL
          D.RKVKSVVTLD.GKLVHVQKW..QET.L
Retrocopy DVRKVKSVVTLDRGKLVHVQKWNRQETML

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	20.13 RPM
SRP017611_kidney	0.00 RPM	80.95 RPM
SRP017611_liver	0.00 RPM	1.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2199 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2199 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016819	2 retrocopies	retro_btau_1467, retro_btau_295,
Danio rerio	ENSDARG00000023290	1 retrocopy	retro_drer_33,
Dasypus novemcinctus	ENSDNOG00000000511	2 retrocopies	retro_dnov_1510, retro_dnov_2482,
Equus caballus	ENSECAG00000024852	1 retrocopy	retro_ecab_519,
Homo sapiens	ENSG00000121769	1 retrocopy	retro_hsap_1258,
Gorilla gorilla	ENSGGOG00000014432	1 retrocopy	retro_ggor_990,
Macropus eugenii	ENSMEUG00000012501	6 retrocopies	retro_meug_1037, retro_meug_148, retro_meug_1660, retro_meug_273, retro_meug_563, retro_meug_819,
Microcebus murinus	ENSMICG00000009359	4 retrocopies	retro_mmur_1490, retro_mmur_203, retro_mmur_621, retro_mmur_734,
Myotis lucifugus	ENSMLUG00000013609	2 retrocopies	retro_mluc_1144, retro_mluc_1717,
Mus musculus	ENSMUSG00000028773	3 retrocopies	retro_mmus_2804, retro_mmus_3204, retro_mmus_65,
Nomascus leucogenys	ENSNLEG00000001586	1 retrocopy	retro_nleu_2097,
Otolemur garnettii	ENSOGAG00000013757	4 retrocopies	retro_ogar_1148, retro_ogar_1312, retro_ogar_1873, retro_ogar_959,
Pongo abelii	ENSPPYG00000001616	1 retrocopy	retro_pabe_1048,
Pan troglodytes	ENSPTRG00000000457	1 retrocopy	retro_ptro_3047,
Rattus norvegicus	ENSRNOG00000012879	1 retrocopy	retro_rnor_2199 ,
Rattus norvegicus	ENSRNOG00000049075	3 retrocopies	retro_rnor_1762, retro_rnor_1879, retro_rnor_1997,
Ictidomys tridecemlineatus	ENSSTOG00000003842	3 retrocopies	retro_itri_1544, retro_itri_640, retro_itri_641,