RetrogeneDB ID: retro_cfam_1426

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:39697787..39698569(-)
• Located in intron of: ENSCAFG00000018100

Retrocopy information

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

Parental gene information

• Parental gene symbol: BSG
• Ensembl ID: ENSCAFG00000019717
• Aliases: None
• Description: basigin (Ok blood group) [Source:HGNC Symbol;Acc:1116]

Sequence

>retro_cfam_1426
GTGGTGCTGGCACAGCTGAGCACTGAGGGCGGCTCTGGGGCAGGGAGCAGGCTCTGGAACTCTGTAGATGATATTGGCTC
CAAAACATGCCTTACCTGCACCTTGAACCATCACGCCACTGAGAGTGTCAGCTACCCGCTGGGTGAAGGGCGGGGGGAGC
AAGTCGCTGAAGGGGGACACATTGCCTGAAGACGGAATATGAGATAGACTTGGATGACCACTCCAGTGAGTACTCATGCA
TCTTCCTCCCAGAACAGGCAGGCAAGACCAGCATTGAAATGAAGGGGCTTCCCAACATCAAGGCCATGAAGTCAGAGCAT
GCCACCGAGGGGAAGACAGTCACGTTGGGCTGTAAGTTGGACTCCTTGCCCCTGGTCAGCAACTGGGTGTGGTACAAGTA
GAAAGCTCCAGGGACCAGGTAATCAGCAACAACTCCCAGAGCAAGTTCTTCATGATGTCCTTGGAGACCAAGAGAGAGCT
GCACATCTCAAACCAGGACCTGGAGGAAGACCCTGGCAAGTATGTCTTCAATGGCACCAACTTGGGAGGGCACCACCAGC
CAGACCATCATTTTGCTGCATGTGCAAAACCGCTCTGCCACCCTCTGGCCCTTCCTGGGTGTTGTGGCCAAGGCACTGGT
GCTGATCACAGTTATTTTCATCTATGAGAAGTGGTGGAAGCCAGACAAGGTCCTGGATGATGATGACATGGGCTTGGCTC
CTCTGAAGGGCAGCAGGCATATGAACACCAAAGGCAAGAACCTTTGCCAGAGGAGGCCCAAC

Alignment

ORF - retro_cfam_1426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.3 %
• Parental protein coverage: 97.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LALALLGAGGGSGAGSEILTSVEDIGSKIRLTCSLNRSTTE-ITGHRWVK--GDRVLKEDTFPD-PKTEY
          ..LA.L...GGSGAGS....SV.DIGSK..LTC.LN...TE.....RWVK..G...LK.DT.P.....E.
Retrocopy VVLAQLSTEGGSGAGSRLWNSVDDIGSKTCLTCTLNHHATE>VSATRWVKGGGSKSLKGDTLPE>TEYEI

Parental  EVDSDERSGEYSCIFLPELLGKSSIEVRGLPNIKAVKKSEHATERETVVLGCRSDSFPPVTDWVWYK-VE
          ..D....S.EYSCIFLPE..GK.SIE..GLPNIKA..KSEHATE..TV.LGC..DS.P.V..WVWYK.VE
Retrocopy DLD--DHSSEYSCIFLPEQAGKTSIEMKGLPNIKAM-KSEHATEGKTVTLGCKLDSLPLVSNWVWYK<VE

Parental  SSGDQVISNSSQSKFLVVSSETKTELRISNLDLETDPGKYVCNGTNS-EGT-SQAVIVLRVRNRFAALWP
          SS.DQVISN.SQSKF...S.ETK.EL.ISN.DLE.DPGKYV.NGTN..EGT.SQ..I.L.V.NR.A.LWP
Retrocopy SSRDQVISNNSQSKFFMMSLETKRELHISNQDLEEDPGKYVFNGTNL>EGTTSQTIILLHVQNRSATLWP

Parental  FLGIVAEVLVLVTVIFIYEKRRKPDEVLDDEDTGSAPLKSSGHVNDKGKNVRQRNAN
          FLG.VA..LVL.TVIFIYEK..KPD.VLDD.D.G.APLK.S.H.N.KGKN..QR..N
Retrocopy FLGVVAKALVLITVIFIYEKWWKPDKVLDDDDMGLAPLKGSRHMNTKGKNLCQRRPN

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	0.00 RPM	227.55 RPM
SRP017611_brain	0.00 RPM	172.36 RPM
SRP017611_kidney	0.00 RPM	1043.52 RPM
SRP017611_liver	0.00 RPM	302.67 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1426 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1426 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1426 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019717	1 retrocopy	retro_cfam_1426 ,
Felis catus	ENSFCAG00000007837	1 retrocopy	retro_fcat_822,
Myotis lucifugus	ENSMLUG00000009184	1 retrocopy	retro_mluc_399,
Monodelphis domestica	ENSMODG00000006517	2 retrocopies	retro_mdom_1195, retro_mdom_1203,
Mustela putorius furo	ENSMPUG00000009950	1 retrocopy	retro_mputfur_878,