RetrogeneDB ID: retro_cfam_585

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:60282690..60283382(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSCAFG00000011617
• Aliases: None
• Description: splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]

Sequence

>retro_cfam_585
CGACTTCCAGCGGCCCAGGACCCCTCTCCCAGGCTGACCGCCCTCACCAGCTGTTTGCAGATGCGCCCCCTCCACCTTCC
GCCCCCAATCCTGTCGTATCATCGTTGGGGTCTGGGCTCCCTCCACCAGGCATGCCTCCTCCTGGGTCCTTCCCACCCCC
AGTGCCGCCTCCTGGAGCCCTTCCACCTGGGATACCCCCAGCCATGCCCCCGCCACCTATGCCTCCTGGGGCTGGAGGAC
ACGGTCCACCATCAGCAGGAACCCCAGGGGCAGACGTCCTGGACATGGACACTCGCAGCCTCGCCCATCCCAGAGTGGGA
CGCCCCATCTAGGGATGTCTCAGTTGCAGTCGGCCCACCACGGCCCTCCTGGCCTAGGACACCCACATGCTGGGCCCCCA
GGCTCGGGGGGGGCAGCCACCACCCCGACCACCACCTGGAATGCCTCATCTGGCCCTCCTCCGATGCGCATGCCCGCTCC
AGGGCCTCCTTTTGGATCTCCCATGGGTCACCCAGGTCCCATGCCTCCACATGGGATACTTGGACCTCCTCCACTAATGC
CTCCTCGTGGATACACTGGGCCTCCATGACCCCCACCCTACGGCTGCCAGTGGGGGCCCCTGCCTCCACCCAGACCCACC
CCCGGGGCCTCCAGTTCCCCCTCGTGGCCCACTCCGAGGCCCTCTTCCTCAG

Alignment

ORF - retro_cfam_585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.65 %
• Parental protein coverage: 54.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RLLAAQN-PLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAM
          RL.AAQ..PLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAM
Retrocopy RLPAAQD<PLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAM

Parental  PPPPMPPGAGGHGPPSAGTPGAG-HPGHGHSHPHPFPPSGMPHPGMSQMQLAHHGPHGLGHPHAGPPG-S
          PPPPMPPGAGGHGPPSAGTPGA...PGHGHS.P.P...SG.PH.GMSQ.Q.AHHGP.GLGHPHAGPPG..
Retrocopy PPPPMPPGAGGHGPPSAGTPGAD<RPGHGHSQPRP-SQSGTPHLGMSQLQSAHHGPPGLGHPHAGPPG>X

Parental  GGQPPPRPPPGMPH-PGPPPMGLPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQR
          ..QPPPRPPPGMPH..GPPPM..P..GPPFGSPMGHPGPMPPHG..GPPPLMPP.GYTGPP.PPPYG.Q.
Retrocopy XXQPPPRPPPGMPH<SGPPPMRMPAPGPPFGSPMGHPGPMPPHGILGPPPLMPPRGYTGPP*PPPYGCQW

Parental  GPLPPPRPT-PRPPVPPRGPLRGPLPQ
          GPLPPPRPT.P.PPVPPRGPLRGPLPQ
Retrocopy GPLPPPRPT>PGPPVPPRGPLRGPLPQ

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
SRP012049_cerebellum	0.04 RPM	40.36 RPM
SRP017611_brain	0.00 RPM	20.96 RPM
SRP017611_kidney	0.00 RPM	23.51 RPM
SRP017611_liver	0.00 RPM	8.77 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_585 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_585 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_585 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_810

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 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,
Canis familiaris	ENSCAFG00000013514	1 retrocopy	retro_cfam_1021,
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,