RetrogeneDB ID: retro_mputfur_1105

Retrocopy location

• Organism: Ferret (Mustela putorius furo)
• Coordinates: GL897017.1:2354745..2356004(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMPUG00000004988
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSMPUG00000005563
• Aliases: None
• Description: splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]

Sequence

>retro_mputfur_1105
GCAGCCAGGCTGATCTCTGAGCAGAACCAGGGTGCTGCTATCTACGTGGGAGGCTTGGATGGGGAGGTTGGCCAACCACG
GCTGTGGGAGCTAATCCTCCAGGCAGGGCCAGTAGTCACCTCCCGCATGCCAAAGGATGAAGTCACAGATCAGCACCAGG
CCAAGGCTTTGTGGAATTCTTGGACAACGAGGAAGCTGACTACACCACGAAGATCATGAACCTGATCAAACTGTGTGGGA
AGGTGGACCAGACATCAGCTCGCAAGAACCTGGATGTGGGGCCAACGTTGTTGTTGGCAACCTGGACTCAGAGATGGATA
GGAAGCTGTTTATGGTATTTCCAGTGCCTTTGGGGTGATTTTACAAACTCCAGAGATTGTGTGGGACCCTAACACAGGCA
ACTCCAAAGATTATGCCTTTATTAATTTTGTTTTGTTTGATGCTTTGGAAGCAGCTGTTCATGTTCTGAATGGGCATTAT
CTCTGTAACCGCCCTATCACTGTGCCCTGTGCCTTTGAGAAGGACTCCAAGGGTCAGCACCAGGGTTCAGCAGCCGAACA
ACTTCTGGCAGCCCAGAACCAACCTACTCTCGCAGGCTGATTGCCCTTGTCAGCTCCTTGCAGAGTCACCCTCTCCACCT
TCAACCCCCAATTCTGTGGCATCATCACTGGGATCTGGGCTTCCTCCCTCAGGTAGCCCTCCTCCTCGGCCCCTCCCACC
CCCAGTGCTGCCTCCTGGAACCATTCTACCTGGGATACCCCCAGCTAGGCCCCCATTACCTGTGTCTCCTGAGGCTGGAG
GACATGGCCCACCATCATCAGGAATGCAGGGTCTGGACATCCTGGACATGGACACTCACATCCTCACCAATTCTCACTGT
ATGGGATGCCCTATCCAGGGATCTCAGATACAGCTGGCCTACCATGGCCCTCATGGGTCAGGACATCCCCATTCCAGGCC
ATCAGGCTCTGGGGGGCAGCCATCACCCCAACCCTCACCTGGCATGCCTCATCTAGGACCTCCTCTAATGGGCATGCCTC
CCGTCCCCCACCAGTGGCCTCTGTTTGGATCTCCCACGCGTCATCCAGGTCTATGCCTCTACATGGGATGCATGGACCTC
CTCCACGGATGCCCCTCATGGATACACTGGGCTTCCACCACCCCCCACCAGATGGCTACCGGTGGGGGCCCCCTCCCTCC
ACCCAGACCAACCCCCGGCCTCTAGTTCTCCTTGTGGCCCACTTTCAGACACTTTTCCT

Alignment

ORF - retro_mputfur_1105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.75 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 12

Retrocopy - Parental Gene Alignment:

Parental  AAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQ-GYGFVEFLSEEDADYA
          AA..ISE.NQ.A..YVGGLD..V..P.LWEL.LQAGPVV...MPKD.VT.QHQ.G.GFVEFL..E.ADY.
Retrocopy AARLISEQNQGAAIYVGGLDGEVGQPRLWELILQAGPVVTSRMPKDEVTDQHQ<GQGFVEFLDNEEADYT

Parental  IKIMNMIKLYGKPIRVNKASAHNKNLDVG-ANIFIGNLDPEIDEKL-LYDTFSAFGVILQTPKIMRDPDT
          .KIMN.IKL.GK...V...SA..KNLDVG.AN...GNLD.E.D.KL..Y...SAFGVILQTP.I..DP.T
Retrocopy TKIMNLIKLCGK---VDQTSAR-KNLDVG<ANVVVGNLDSEMDRKL<VYGISSAFGVILQTPEIVWDPNT

Parental  GNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAER-LLAAQNP-LSQADR
          GNSK.YAFINF..FDA..AA....NG.YLCNRPITV..AF.KDSKG...GSAAE..L.A...P.LSQAD.
Retrocopy GNSKDYAFINFVLFDALEAAVHVLNGHYLCNRPITVPCAFEKDSKGQHQGSAAEQLLAAQNQP>LSQADC

Parental  PHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPP
          P.QL.A..P.PPS.PN.V.SSLGSGLPP.G.PPP...PPPV.PPG...PGIPPA.PP.P..P.AGGHGPP
Retrocopy PCQLLAESPSPPSTPNSVASSLGSGLPPSGSPPPRPLPPPVLPPGTILPGIPPARPPLPVSPEAGGHGPP

Parental  SAG-TPGAGHPGHGHSHPHPFPPGGM-PHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHP
          S.G...G.GHPGHGHSHPH.F...GM.P..G.SQ.QLA.HGPHG.GHPH..P.GSGGQP.P.P.PGMPH.
Retrocopy SSG<NAGSGHPGHGHSHPHQFSLYGM>PIQG-SQIQLAYHGPHGSGHPHSRPSGSGGQPSPQPSPGMPHL

Parental  GPPPMGMPP---RGPPFGSPMGHPG-PMPPHGMRGPPPLMP-PHGYTGPP-RPPPYGYQ-RGPLPPPRPT
          GPP.MGMPP.....P.FGSP..HPG..MP.HGM.GPPP.MP.PHGYTG.P..PPP.GY...GPLPPPRPT
Retrocopy GPPLMGMPPVPHQWPLFGSPTRHPG<SMPLHGMHGPPPRMP<PHGYTGLP>HPPPDGYR>GGPLPPPRPT

Parental  -PRPPV-PPRGPLRGPLP
          .PRP.V..P.GPL....P
Retrocopy <PRPLV<SPCGPLSDTFP

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_1105 retrocopy.

TSS

Mustela putorius furo was not studied using FANTOM5 data.

Lab

retro_mputfur_1105 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 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012495	2 retrocopies	retro_btau_1385, retro_btau_592,
Canis familiaris	ENSCAFG00000011617	3 retrocopies	retro_cfam_585, retro_cfam_711, retro_cfam_729,
Callithrix jacchus	ENSCJAG00000000793	3 retrocopies	retro_cjac_1297, retro_cjac_1909, retro_cjac_638,
Cavia porcellus	ENSCPOG00000008267	1 retrocopy	retro_cpor_234,
Echinops telfairi	ENSETEG00000008963	1 retrocopy	retro_etel_1310,
Homo sapiens	ENSG00000143368	1 retrocopy	retro_hsap_1356,
Gorilla gorilla	ENSGGOG00000004761	1 retrocopy	retro_ggor_1056,
Macaca mulatta	ENSMMUG00000007256	1 retrocopy	retro_mmul_2191,
Mustela putorius furo	ENSMPUG00000005563	2 retrocopies	retro_mputfur_1105 , retro_mputfur_648,
Oryctolagus cuniculus	ENSOCUG00000004614	1 retrocopy	retro_ocun_1239,
Pongo abelii	ENSPPYG00000000912	1 retrocopy	retro_pabe_1124,
Pan troglodytes	ENSPTRG00000001243	1 retrocopy	retro_ptro_930,
Pteropus vampyrus	ENSPVAG00000014171	1 retrocopy	retro_pvam_931,
Rattus norvegicus	ENSRNOG00000021181	1 retrocopy	retro_rnor_2350,
Ictidomys tridecemlineatus	ENSSTOG00000000684	2 retrocopies	retro_itri_1153, retro_itri_487,