RetrogeneDB ID: retro_rnor_1407

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:69559878..69560195(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Edf1
• Ensembl ID: ENSRNOG00000016272
• Aliases: Edf1, CAP-19
• Description: Endothelial differentiation-related factor 1 [Source:UniProtKB/Swiss-Prot;Acc:P69736]

Sequence

>retro_rnor_1407
AAGTCTAAGCAGGCCATCTTAGCAGCTCAGCGATGAGGAGAAGATGTGGAGACATCCAAGAAATGGGCTGCTGGCCAGAA
CAAGCAGCATTCCATCACTAAAAACACAGCCAAGCTAGACCGGGCAACAGAGGAACTACATCGGGACAGGGTGACCCAGG
GGGTGGGCAAAGTGATCCTGCAGGCTGGCAGAGCAAAGGCCTGACGTAGAAGGACCTGGCCATGAAAATCAATGAAAATC
CTCAAGTCATCGCAGACTATGAAAGTGGACAGGCCATTCCGAATAACCAGGTTTTGGGCAAAATTGAGAGAGCCATC

Alignment

ORF - retro_rnor_1407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 71.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSKQAILAAQRRGEDVETSKKWAAGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQR-GRQSKGLT
          KSKQAILAAQR.GEDVETSKKWAAGQNKQHSITKNTAKLDR.TEELH.DRVT..VGKVI...G.QSKGLT
Retrocopy KSKQAILAAQR*GEDVETSKKWAAGQNKQHSITKNTAKLDRATEELHRDRVTQGVGKVILQ<GWQSKGLT

Parental  QKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAI
          .KDLA.KINE.PQVIADYESG.AIPNNQVLGKIERAI
Retrocopy *KDLAMKINENPQVIADYESGQAIPNNQVLGKIERAI

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	57.73 RPM
SRP017611_kidney	0.00 RPM	76.97 RPM
SRP017611_liver	0.00 RPM	31.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1407 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1407 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1407 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013266	2 retrocopies	retro_amel_1569, retro_amel_996,
Canis familiaris	ENSCAFG00000019544	4 retrocopies	retro_cfam_1283, retro_cfam_1812, retro_cfam_363, retro_cfam_895,
Callithrix jacchus	ENSCJAG00000011166	1 retrocopy	retro_cjac_374,
Erinaceus europaeus	ENSEEUG00000009565	1 retrocopy	retro_eeur_635,
Loxodonta africana	ENSLAFG00000026812	1 retrocopy	retro_lafr_751,
Macropus eugenii	ENSMEUG00000015037	7 retrocopies	retro_meug_108, retro_meug_1742, retro_meug_1805, retro_meug_2070, retro_meug_38, retro_meug_598, retro_meug_773,
Microcebus murinus	ENSMICG00000016498	1 retrocopy	retro_mmur_312,
Macaca mulatta	ENSMMUG00000005051	1 retrocopy	retro_mmul_89,
Monodelphis domestica	ENSMODG00000017329	1 retrocopy	retro_mdom_1713,
Mustela putorius furo	ENSMPUG00000011008	1 retrocopy	retro_mputfur_1377,
Mus musculus	ENSMUSG00000015092	3 retrocopies	retro_mmus_3324, retro_mmus_688, retro_mmus_809,
Rattus norvegicus	ENSRNOG00000016272	4 retrocopies	retro_rnor_1407 , retro_rnor_2005, retro_rnor_2007, retro_rnor_2616,
Sorex araneus	ENSSARG00000007191	1 retrocopy	retro_sara_39,
Tupaia belangeri	ENSTBEG00000014060	4 retrocopies	retro_tbel_1404, retro_tbel_1950, retro_tbel_3538, retro_tbel_967,
Tursiops truncatus	ENSTTRG00000002668	2 retrocopies	retro_ttru_165, retro_ttru_894,