RetrogeneDB ID: retro_mputfur_1073

Retrocopy location

• Organism: Ferret (Mustela putorius furo)
• Coordinates: GL897007.1:1203101..1203868(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFC3
• Ensembl ID: ENSMPUG00000001885
• Aliases: None
• Description: replication factor C (activator 1) 3, 38kDa [Source:HGNC Symbol;Acc:9971]

Sequence

>retro_mputfur_1073
ATAAGCCTCTGGGTGAACAAATACCGGCCCTGCTCCTTGGGAAGGCTGGACTCTCACGAGGAGCAGGCGGCCCAGCTGCG
CAACCTGGTGCAGTGTGGTGATTTTCCTCATCTCTTAGTGTATGGACCATCAGGGGCTGGAAAAAAGACAAGAATTATGT
GTATTCTATGTGAACTTTATGGTGTTGGAGTCGAAACATTAAGAGTTGAACATCAGACCATCACAACTCCATCTAAAAAG
AAAATTGAAATTAGCACTATTGGGAGCAATTGAAGCACCTTGAAGTGAATCCCAGTGATGCTGGAAATAGTGACCGGGTA
GTAATTCAGGAGATGTTGAAAACAGTGGCATGATCACAGCAACTTGAAACAAATTCTCAAAGAGATTTTAAAGTGGTATT
ATTGACAGAGGTTGTCAGACTCACCAAAGACGCTCAACATGCCTTGCGTAGGACCATGGAAAGGTATATGTCCACTTGTA
GATTGATCTTGTGTTGCAATTCTACATCTAAAGTGGTACCACCTATTCGCAGTAGGTGCCTGCGGGTTCGTGTGCCTGCT
CCCAACATCGAAGATATTCATCACGTATTATCTACTGTGTGCAAGAAGGAAGGTTTGAATCTTCCTTCACAACTGGCTCA
TAGACTTGCAGAGAAGTCCTGCAGGAATCTCCGTAAAGCTCTACTTATGTGTGAAGCCTGCAGAGAGCAACAATACCCTT
TTAGTGCAGATCAAGAAATCCCTGAAACAGATTGGGAGGTGTTATTG

Alignment

ORF - retro_mputfur_1073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.94 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSLWVDKYRPCSLGRLDYHKELAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGVGVEKLRIE
          .SLWV.KYRPCSLGRLD.H.E.AAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCIL.ELYGVGVE.LR.E
Retrocopy ISLWVNKYRPCSLGRLDSHEEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILCELYGVGVETLRVE

Parental  HQTITTPSK-KKIEISTIASNY-HLEVNPSDAGNSDRVVIQEMLKTVAQSQQLETNSQRDFKVVLLTEVD
          HQTITTPSK..K...........HLEVNPSDAGNSDRVVIQEMLKTVA.SQQLETNSQRDFKVVLLTEV.
Retrocopy HQTITTPSK>RKLKLALLGAIE>HLEVNPSDAGNSDRVVIQEMLKTVA*SQQLETNSQRDFKVVLLTEVV

Parental  KLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLP
          .LTKDAQHALRRTME.YMSTCRLILCCNSTSKV.PPIRSRCL.VRVPAP.IEDI.HVLSTVCKKEGLNLP
Retrocopy RLTKDAQHALRRTMERYMSTCRLILCCNSTSKVVPPIRSRCLRVRVPAPNIEDIHHVLSTVCKKEGLNLP

Parental  SQLAHRLAEKSCRNLRKALLMCEACRVQQYPFSADQEIPETDWEVYL
          SQLAHRLAEKSCRNLRKALLMCEACR.QQYPFSADQEIPETDWEV.L
Retrocopy SQLAHRLAEKSCRNLRKALLMCEACREQQYPFSADQEIPETDWEVLL

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_1073 retrocopy.

TSS

Mustela putorius furo was not studied using FANTOM5 data.

Lab

retro_mputfur_1073 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018380	1 retrocopy	retro_cjac_1611,
Cavia porcellus	ENSCPOG00000008739	1 retrocopy	retro_cpor_405,
Myotis lucifugus	ENSMLUG00000014088	1 retrocopy	retro_mluc_1754,
Mustela putorius furo	ENSMPUG00000001885	1 retrocopy	retro_mputfur_1073 ,
Nomascus leucogenys	ENSNLEG00000001169	1 retrocopy	retro_nleu_674,
Pongo abelii	ENSPPYG00000005272	1 retrocopy	retro_pabe_2420,
Tupaia belangeri	ENSTBEG00000004725	1 retrocopy	retro_tbel_4191,
Tarsius syrichta	ENSTSYG00000009501	2 retrocopies	retro_tsyr_1772, retro_tsyr_331,