RetrogeneDB ID: retro_cfam_707

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:39456730..39457605(+)
• Located in intron of: ENSCAFG00000006830

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANXA2
• Ensembl ID: ENSCAFG00000016686
• Aliases: None
• Description: Canis lupus familiaris annexin A2 (ANXA2), mRNA. [Source:RefSeq mRNA;Acc:NM_001002961]

Sequence

>retro_cfam_707
ATGTCTCCTGTTCACGAAATTCTCTGCAAGCTCAGCTTGGAGGGTGATCACTCCATGCCCCCAAGTGCATACAGGTTGGT
CAAAGCACACACCAATTTTGATGCTGAGCGTGATGCTCGGAACATTGAAGCAGCCATCAAGACCAAAGGTGTGGATGAGG
TCACCATTGTCAACATTTTGACCAACCACAGCAATGAACAGAGACAGGACATTGCCTTCGCCTACCAGAGAAGGACCAAA
AAGGAACTTGCATCAACATTGCAGTCAGCCTTGTCTGGCCACCTGGAGACCGTGATTTGGGGCCTATTGAAAACACGTGC
TCAGTATGACACTTCTGAACTGAAAGGCTCCATGAAGGGGCTGGGAACTGATAAGGAGTCCTTCATTGAGATCATCTGCT
CAAGGACCAACCAGGAACTTTAGGAAATTAACAGAGTCTACAAGGAAATGTATAAGACCAATCTGGAGAAGGACATCATT
TCTGACACATCTGGTGACTTCCGCAAGCTGATGGTTGCCCTTGCAAAGGGTAGAAGAGCAGAGGATTGCTCTGTCCTTGA
TTATGAACTGATTGGCCAAGATGCCTGGGATCTCTATGATGCTGGAGTGAAGAGGAAAGGAACTGATGTGCCCAAGTGGA
TTGGCATCATGACTGAGAGGAATGTATGTCACCTCCAGAAAGTATTTGAAAGGGACAAGAGCTACAGCTCTTATGACATG
CTGGAGAGCATCAAGAAGGAAGTCCAAGGAGACCTGGAAAATGCTTTCCTGAACCTGATCCAGTGCATTCAGAACAAGCC
CCTGTATTTTGCCGACTGACTGTACGACTCCATGAAGGGCAAGGGGACTCGTGATAAGTCCTGACTAGAATCATG

Alignment

ORF - retro_cfam_707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.08 %
• Parental protein coverage: 86.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTVHEILCKLSLEGDHSTPPSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQD
          MS.VHEILCKLSLEGDHS.PPSAY..VKA.TNFDAERDA.NIE.AIKTKGVDEVTIVNILTN.SNEQRQD
Retrocopy MSPVHEILCKLSLEGDHSMPPSAYRLVKAHTNFDAERDARNIEAAIKTKGVDEVTIVNILTNHSNEQRQD

Parental  IAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQEL
          IAFAYQRRTKKELAS.L.SALSGHLETVI.GLLKT.AQYD.SELK.SMKGLGTD..S.IEIICSRTNQEL
Retrocopy IAFAYQRRTKKELASTLQSALSGHLETVIWGLLKTRAQYDTSELKGSMKGLGTDKESFIEIICSRTNQEL

Parental  QEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDV
          .EINRVYKEMYKT.LEKDIISDTSGDFRKLMVALAKGRRAED.SV.DYELI.QDA.DLYDAGVKRKGTDV
Retrocopy *EINRVYKEMYKTNLEKDIISDTSGDFRKLMVALAKGRRAEDCSVLDYELIGQDAWDLYDAGVKRKGTDV

Parental  PKWISIMTERSVCHLQKVFERYKSYSPYDMLESIKKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKG
          PKWI.IMTER.VCHLQKVFER.KSYS.YDMLESIKKEV.GDLENAFLNL.QCIQNKPLYFAD.LYDSMKG
Retrocopy PKWIGIMTERNVCHLQKVFERDKSYSSYDMLESIKKEVQGDLENAFLNLIQCIQNKPLYFAD*LYDSMKG

Parental  KGTRDK-VLIRIM
          KGTRDK.VL.RIM
Retrocopy KGTRDK<VLTRIM

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	20.12 RPM
SRP017611_brain	0.00 RPM	18.02 RPM
SRP017611_kidney	0.00 RPM	99.39 RPM
SRP017611_liver	0.00 RPM	9.86 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_707 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_707 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_707 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008055	2 retrocopies	retro_amel_1531, retro_amel_1836,
Bos taurus	ENSBTAG00000009615	2 retrocopies	retro_btau_634, retro_btau_985,
Canis familiaris	ENSCAFG00000014749	1 retrocopy	retro_cfam_1107,
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707 ,
Choloepus hoffmanni	ENSCHOG00000012143	3 retrocopies	retro_chof_1028, retro_chof_1965, retro_chof_815,
Equus caballus	ENSECAG00000012670	1 retrocopy	retro_ecab_759,
Felis catus	ENSFCAG00000007862	2 retrocopies	retro_fcat_594, retro_fcat_709,
Homo sapiens	ENSG00000182718	3 retrocopies	retro_hsap_3114, retro_hsap_4150, retro_hsap_580,
Gorilla gorilla	ENSGGOG00000009738	3 retrocopies	retro_ggor_2137, retro_ggor_2788, retro_ggor_515,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Myotis lucifugus	ENSMLUG00000002464	3 retrocopies	retro_mluc_1569, retro_mluc_2223, retro_mluc_2431,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Nomascus leucogenys	ENSNLEG00000011678	2 retrocopies	retro_nleu_769, retro_nleu_802,
Otolemur garnettii	ENSOGAG00000009952	1 retrocopy	retro_ogar_3510,
Pongo abelii	ENSPPYG00000006526	2 retrocopies	retro_pabe_2572, retro_pabe_607,
Pan troglodytes	ENSPTRG00000007132	2 retrocopies	retro_ptro_2106, retro_ptro_81,
Pteropus vampyrus	ENSPVAG00000011401	1 retrocopy	retro_pvam_389,
Tupaia belangeri	ENSTBEG00000001276	1 retrocopy	retro_tbel_3335,
Tarsius syrichta	ENSTSYG00000003719	1 retrocopy	retro_tsyr_2086,
Tursiops truncatus	ENSTTRG00000007705	1 retrocopy	retro_ttru_1725,
Vicugna pacos	ENSVPAG00000007888	2 retrocopies	retro_vpac_241, retro_vpac_27,