RetrogeneDB ID: retro_cfam_211

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:36286583..36287489(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000006109
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000005955
• Aliases: None
• Description: None

Sequence

>retro_cfam_211
ATGAAGTCCAACCCTGCCGTCCAAGCCGCCATCGACCTCACCGCGGGTGCCGTTGGGGGCACGGCGTGTGTCCTGACCGG
GCAGCCTTTCGACACAGTGAAAGTGAAGATGCAGACGTTCCCCGGCCTGTACAAGGGCCTCGTGGACTGCTGCCTGAAAA
CGTACTCCCAAGTGGGCTTTCGGGGCTTCTACAAGGGAACCGGCCCCGCGCTGATGGCCTACGTCGCCGAGAACTCTGTC
CTCTTCATGTGCTATGGCTTCTGCCAACAGCTCGTGAGGAAGGTGGTGGGATTGGACGAGCAGGAGAAGCTGACCGATCT
GCAGGCGGCAGCTGCGGGTTCCTTCGCCTCCGCGTTTGCCGCGCTGGCCCTGTGTCCCACTGAGCTTGTGAAGTGCCGGC
TACAGACTATGTACGAAATGGAGATGTCAGGGAAAATAGCAAAAAGCCAAAATACAATCTGGTCCGTCGTGAAAAGTATC
CTTAGAAAGGAAGGCCCCTTGGGCTTCTACCACGGACTTTCGAGCACTCTACTTCAGGAAGTACCAGGCTATTTCTTCTT
CTTCTGTGGCTATGAACTGAGTCGGTCATTTTTTGCCTCCGGGAGATCAAAAGATGAACTAGGCCCTGTCCCTTTGATGT
TAAGTGGTGGAATTGCTGGAATTTGTCTTTGGCTTGTCATATACCCAGTGGATTGTATCAAATCCAGAATTCAGGTTCTT
TCCATATCTGGAAAACAGGCTGGGTTTCTGGGAACGCTTCTAAGTGTGGTGAAAAATGAAGGAACAGCAGCTTTATATTC
TGGGCTGACAGCTACTATGATTCGAGCGTTCCCTGCCAATGGGTCACTATTTTTGGCTTATGAATATAGTAGGAGAATGA
TGATGAACCAGTTTGAAGCATACTGA

Alignment

ORF - retro_cfam_211 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKPNPAIQAAIDLTAGAAGGTACVLTGQPFDTLKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPA
          MK.NPA.QAAIDLTAGA.GGTACVLTGQPFDT.KVKMQTFP.LY.GL.DCCLKTYSQVGFRGFYKGT.PA
Retrocopy MKSNPAVQAAIDLTAGAVGGTACVLTGQPFDTVKVKMQTFPGLYKGLVDCCLKTYSQVGFRGFYKGTGPA

Parental  LIANIAENSVLFMCYGFCQQVVRKVVGLEKQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMHEM
          L.A..AENSVLFMCYGFCQQ.VRKVVGL..Q.KL.DLQ.AAAGSFASAFAAL.LCPTELVKCRLQTM.EM
Retrocopy LMAYVAENSVLFMCYGFCQQLVRKVVGLDEQEKLTDLQAAAAGSFASAFAALALCPTELVKCRLQTMYEM

Parental  ASSGKIANSQNTVWSVVKTVLRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGKSKDELGPV
          ..SGKIA.SQNT.WSVVK..LRK.GPLGFYHGLSSTLL.EVPGYFFFF.GYELSRSFFASG.SKDELGPV
Retrocopy EMSGKIAKSQNTIWSVVKSILRKEGPLGFYHGLSSTLLQEVPGYFFFFCGYELSRSFFASGRSKDELGPV

Parental  PLMLSGGVGGVCLWLAVYPVDCVKSRIQVLSMSGKQAGFIGTFISIVKNEGITALYSGLKPTMIRAFPAN
          PLMLSGG..G.CLWL..YPVDC.KSRIQVLS.SGKQAGF.GT..S.VKNEG..ALYSGL..TMIRAFPAN
Retrocopy PLMLSGGIAGICLWLVIYPVDCIKSRIQVLSISGKQAGFLGTLLSVVKNEGTAALYSGLTATMIRAFPAN

Parental  GALFLAYEYSRKLMMSQFEAY
          G.LFLAYEYSR..MM.QFEAY
Retrocopy GSLFLAYEYSRRMMMNQFEAY

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	8.19 RPM
SRP017611_brain	0.00 RPM	4.29 RPM
SRP017611_kidney	0.07 RPM	24.96 RPM
SRP017611_liver	0.00 RPM	75.12 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_211 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_211 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211 ,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494, retro_chof_561,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192, retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688,