RetrogeneDB ID: retro_rnor_1392

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:35610353..35610847(-)
• Located in intron of: ENSRNOG00000046709

Retrocopy information

• Ensembl ID: ENSRNOG00000050115
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Skp1
• Ensembl ID: ENSRNOG00000005828
• Aliases: Skp1, Skp1a
• Description: S-phase kinase-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q6PEC4]

Sequence

>retro_rnor_1392
ATGCCTACAATAAAGTTGCAGAGTTCTGATGGAGAGATATTTGAAGTTGATGTACAAATTGCCAAACAATCTGTGACCAT
TAAGACCATGCTGGAAGATATGGGAATGGATGACGAGGGAGCTGATGGTCCTGGTCCTTTATCAAATGTTAGTGCAGCAA
TTCTAAAAGAAGGTCCTTCAGTGGTGCACCCAGCAGAAGGATGGCCCTCTGCTCTGAGGATGAGGAGAACAAAGAAAAGC
GGACTGATGATATCACTGTTCAGGACCAAGGGTTCCTAAAAGTTGACCAAGGAACACTACTTGAACTTATTCTGGCTGCA
AATTACTTAGACATTAAAGGTTTGCTTGATGTCACCTGGAAGACTGTGGCCAATATGATTAAGGGGAAAACTCTTGAGAA
GATTCGTAAAACCTTCCATATCAAAAATGACTTCACTGTAGAGGTAGAGGCAGAGGCCCAGGTACCCAAAGAAAATCAAC
AGTGTGAAGAGAAG

Alignment

ORF - retro_rnor_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPTIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAIL-KKVIQWCTHHKDDP
          MPTIKLQSSDGEIFEVDV.IAKQSVTIKTMLED.GMDDEG.D.P.PL.NV.AAIL.KKV.QWCT..KD.P
Retrocopy MPTIKLQSSDGEIFEVDVQIAKQSVTIKTMLEDMGMDDEGADGPGPLSNVSAAIL>KKVLQWCTQQKDGP

Parental  -PPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKT
          ..............D.I.V.DQ.FLKVDQGTL.ELILAANYLDIKGLLDVT.KTVANMIKGKT.E.IRKT
Retrocopy >CSEDEENKEKRTDD-ITVQDQGFLKVDQGTLLELILAANYLDIKGLLDVTWKTVANMIKGKTLEKIRKT

Parental  FNIKNDFT--EEEEAQVRKENQWCEEK
          F.IKNDFT...E.EAQV.KENQ.CEEK
Retrocopy FHIKNDFTVEVEAEAQVPKENQQCEEK

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	277.95 RPM
SRP017611_kidney	0.00 RPM	493.22 RPM
SRP017611_liver	0.00 RPM	143.96 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1392 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1392 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025191	5 retrocopies	retro_btau_10, retro_btau_1062, retro_btau_1253, retro_btau_1444, retro_btau_1687,
Canis familiaris	ENSCAFG00000000994	5 retrocopies	retro_cfam_1613, retro_cfam_779, retro_cfam_813, retro_cfam_889, retro_cfam_965,
Callithrix jacchus	ENSCJAG00000013613	1 retrocopy	retro_cjac_112,
Echinops telfairi	ENSETEG00000007560	5 retrocopies	retro_etel_1730, retro_etel_515, retro_etel_758, retro_etel_762, retro_etel_811,
Homo sapiens	ENSG00000113558	10 retrocopies	retro_hsap_2193, retro_hsap_2596, retro_hsap_3321, retro_hsap_3346, retro_hsap_3863, retro_hsap_4161, retro_hsap_4163, retro_hsap_4164, retro_hsap_724, retro_hsap_972,
Gorilla gorilla	ENSGGOG00000022930	7 retrocopies	retro_ggor_1288, retro_ggor_1300, retro_ggor_2601, retro_ggor_2602, retro_ggor_2796, retro_ggor_2797, retro_ggor_778,
Loxodonta africana	ENSLAFG00000016832	1 retrocopy	retro_lafr_83,
Microcebus murinus	ENSMICG00000017588	3 retrocopies	retro_mmur_270, retro_mmur_803, retro_mmur_997,
Myotis lucifugus	ENSMLUG00000022919	13 retrocopies	retro_mluc_1455, retro_mluc_1738, retro_mluc_1895, retro_mluc_2009, retro_mluc_2260, retro_mluc_2261, retro_mluc_2520, retro_mluc_2527, retro_mluc_2557, retro_mluc_267, retro_mluc_383, retro_mluc_841, retro_mluc_944,
Monodelphis domestica	ENSMODG00000014168	4 retrocopies	retro_mdom_1173, retro_mdom_155, retro_mdom_1648, retro_mdom_929,
Otolemur garnettii	ENSOGAG00000028707	8 retrocopies	retro_ogar_1446, retro_ogar_1510, retro_ogar_1511, retro_ogar_1890, retro_ogar_2019, retro_ogar_2728, retro_ogar_3306, retro_ogar_581,
Pongo abelii	ENSPPYG00000015783	7 retrocopies	retro_pabe_1915, retro_pabe_199, retro_pabe_2072, retro_pabe_2736, retro_pabe_2756, retro_pabe_626, retro_pabe_824,
Rattus norvegicus	ENSRNOG00000005828	6 retrocopies	retro_rnor_1391, retro_rnor_1392 , retro_rnor_1465, retro_rnor_1888, retro_rnor_2166, retro_rnor_2333,