RetrogeneDB ID: retro_mputfur_293

Retrocopy location

• Organism: Ferret (Mustela putorius furo)
• Coordinates: GL896901.1:33273874..33274531(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSMPUG00000013922
• Aliases: None
• Description: Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]

Sequence

>retro_mputfur_293
CCCCAGAGAGCCCTGAGCAGCCCTATCAACCCCCACTGGCCTTGTTATCATCACACCTGGGGAGACAGCCACAGCTGCCA
CGGACTCACATCCTGGCCTGCCATTGGGGATAAGAAGGTCATCACAAGGAAGATTTTGGGAACAGTAAAATGGTTGAGTG
TGAGAAATGGGTATGGCTTCATCAACAGGAATGACAGCAAGGAAGATGTGTTTGTATACCAGACTGCCATAAAGAACAAT
AATCCTGGGAGGCGCCGTCCCAGTGGAGGAGGTGGAGAGATGGTGTAGTTGGATGTTGTCGAAGGAGAAAAGGGTGTGGA
GGCGGCAAATGTGATAGGCTGTTGTTGAGTTCCAGTGCAAGGCAGTAAATATGCAGCAGACTGGAACCATCATAGACATT
CTCCACGATGCCGGGGTCCTCCACACATTTACCAGCAGAATTACAGAACAGTGAGAGTGGGGAAAAGGAGGGTTGGGAAA
GTGTTCCTGAAGGCCAGGTCCCAACAGCACCAGCCCTACCACCGGTGACAGTTCCCACCTTACTGCATGTGCAGACCCTC
TGGGTATCAACCACAGTCTTCCAATCCTCCTTTGTGGGGAGAAGTGATGGAAGGTGCTGACAACCAGGATGCAGGAGAAC
AAGACTGACCAGTGAGA

Alignment

ORF - retro_mputfur_293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.99 %
• Parental protein coverage: 65.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PARALSQSL--HRP--HGALARGGTAGGAVAAPAGPDSKTLESLILGKVKWHQINNGWLFLRRLNDTKED
          P.RALS.....H.P..H..........G....PA..D.K.....ILG.VKW....NG..F..R.ND.KED
Retrocopy PQRALSSPINPHWPCYHHTWGDSHSCHGLTSWPAIGDKKVITRKILGTVKWLSVRNGYGFINR-NDSKED

Parental  VFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRHRG
          VFV.QTAIK.NNP.....S.G.GE.V..DVVEGEKG.EAANV.G...VPVQGSKYAAD.NH.R..PR.RG
Retrocopy VFVYQTAIKNNNPGRRRPSGGGGEMV*LDVVEGEKGVEAANVIGCC*VPVQGSKYAADWNHHRHSPRCRG

Parental  PPHNYQQNY-QNSESGEKNEGSESAPEGQ-AQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGA
          PPH.YQQNY.QNSESGEK.EG.ES.PEGQ..QQ..PY.R..FPPY.M.RP.G..PQ.SNPP..GEVMEGA
Retrocopy PPHIYQQNY<QNSESGEK-EGWESVPEGQ>SQQHQPYHR*QFPPYCMCRPSGYQPQSSNPPLWGEVMEGA

Parental  DNQGAGEQGRPVR
          DNQ.AGEQ..PVR
Retrocopy DNQDAGEQD*PVR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Mustela putorius furo was not studied using RNA-Seq expression data.

ChIP-Seq

Mustela putorius furo was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mputfur_293 retrocopy.

TSS

Mustela putorius furo was not studied using FANTOM5 data.

Lab

retro_mputfur_293 was not experimentally validated.

Homology

Retrocopy orthology:

Mustela putorius furo does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000004125	3 retrocopies	retro_etel_1772, retro_etel_1980, retro_etel_2134,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Mustela putorius furo	ENSMPUG00000013922	6 retrocopies	retro_mputfur_1154, retro_mputfur_1332, retro_mputfur_1436, retro_mputfur_1627, retro_mputfur_215, retro_mputfur_293 ,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Ochotona princeps	ENSOPRG00000008050	11 retrocopies	retro_opri_1097, retro_opri_1114, retro_opri_115, retro_opri_1196, retro_opri_340, retro_opri_367, retro_opri_626, retro_opri_781, retro_opri_896, retro_opri_910, retro_opri_984,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,