RetrogeneDB ID: retro_cfam_2012

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:54212334..54213081(-)
• Located in intron of: ENSCAFG00000019983

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000019472
• Aliases: None
• Description: None

Sequence

>retro_cfam_2012
ATAGTAGATGATACTGGTGCTGCAGGAGGGCCTGGAGGACCCAGGTGCCCCAGAATGGGGGGCCAGTGGCTTCCATGGAG
GCTTCAGCAATGGCATCTGGGGCCAGAGTCAGGGCCATAGTCAGGGAGGCCACAGAGCTCTCAGGAGCAAGGCTGAGGAC
AAGGAGTAGATCCCTGACACCAAGCTGGGCCACCCTGGTCAAAGTCATGAAGATTAAGTCCCTGGAGGAGATCTATCTCT
TCTCTCTGCTCATCAGGGAATCTGCGATCATTGAATTTTTCCTGGGAGCACCCTCAAGGATGAAGTTTTGAAAATTATGC
CTGTGCAAAAGCAGATCTGTGCTGGCCAGTGGACCAGGTTCAAGGTATTTGTTGCCATCAGGAATTACAATGAACACATC
AGTCTGGATGTTAAGAGCTCCAGGAAGGTAGCCACCGCCATCGGTGGGGCCATCACCCTGGCCAAGCCTTCTACCATCCT
ATGCGGCAAGGCTACTGGGGAAACAAGATTGGCAAGCCCCACATTATTTCATGCAAGGTGACCAGGCTCTGTGGCTCTGT
GCTGATGCTCCTCATCCCCAACACCAGGGACACTGGCATTGTCTCAGCCCCTCTGCCCAAGAAGCTATTGATGATGGCTG
ATATTGACGATGGCTACACCTCAGCCACGGACTGCACTGCCACCCAGGGCGATCATGCCAAGGCCACATGTGATGCCATT
CCTAAGATCTACAGCTGTCATACCCCA

Alignment

ORF - retro_cfam_2012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.7 %
• Parental protein coverage: 86.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAGGPGGP-GGPGMGGRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEWIPVTKLGR-
          ..DD.GAAGGPGGP.G.P..G...GF.GGF..GI.G...G...G...G..A...KAEDKE.IP.TKLG..
Retrocopy IVDDTGAAGGPGGP>GAPEWGA-SGFHGGFSNGIWGQSQGHSQG---GHRALRSKAEDKE*IPDTKLGH>

Parental  LVKDMKIKSLEEIYLFSLPIKESEIIDFFLGA-SLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHV
          LVK.MKIKSLEEIYLFSL.I.ES.II.FFLGA..LKDEVLKIMPVQKQ..AGQ.TRFK.FVAI..YN.H.
Retrocopy LVKVMKIKSLEEIYLFSLLIRESAIIEFFLGA<TLKDEVLKIMPVQKQICAGQWTRFKVFVAIRNYNEHI

Parental  GLGVKCSKEVATAIRGAIILAKLSIV-PVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVS
          .L.VK.S..VATAI.GAI.LAK.S...P.R.GYWGNKIGKPH...CKVT..CGSVL..LIP..R.TGIVS
Retrocopy SLDVKSSRKVATAIGGAITLAKPSTI<PMRQGYWGNKIGKPHIISCKVTRLCGSVLMLLIPNTRDTGIVS

Parental  APVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTP
          AP.PKKLLMMA.IDD.YTSA..CTAT.G..AKAT.DAI.K.YS..TP
Retrocopy APLPKKLLMMADIDDGYTSATDCTATQGDHAKATCDAIPKIYSCHTP

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	405.33 RPM
SRP017611_brain	0.00 RPM	141.00 RPM
SRP017611_kidney	0.00 RPM	1239.39 RPM
SRP017611_liver	0.00 RPM	306.08 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2012 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2012 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Bos taurus	ENSBTAG00000009535	7 retrocopies	retro_btau_1236, retro_btau_1420, retro_btau_1656, retro_btau_317, retro_btau_590, retro_btau_661, retro_btau_956,
Canis familiaris	ENSCAFG00000019472	19 retrocopies	retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012 , retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Equus caballus	ENSECAG00000009065	7 retrocopies	retro_ecab_1025, retro_ecab_1105, retro_ecab_509, retro_ecab_632, retro_ecab_876, retro_ecab_892, retro_ecab_949,
Loxodonta africana	ENSLAFG00000004696	11 retrocopies	retro_lafr_1072, retro_lafr_1092, retro_lafr_1103, retro_lafr_174, retro_lafr_284, retro_lafr_327, retro_lafr_376, retro_lafr_75, retro_lafr_801, retro_lafr_812, retro_lafr_917,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Mus musculus	ENSMUSG00000044533	1 retrocopy	retro_mmus_148,
Procavia capensis	ENSPCAG00000002090	2 retrocopies	retro_pcap_251, retro_pcap_433,
Pteropus vampyrus	ENSPVAG00000016704	8 retrocopies	retro_pvam_1395, retro_pvam_1486, retro_pvam_221, retro_pvam_240, retro_pvam_34, retro_pvam_459, retro_pvam_521, retro_pvam_595,
Rattus norvegicus	ENSRNOG00000014179	12 retrocopies	retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tursiops truncatus	ENSTTRG00000011393	12 retrocopies	retro_ttru_1341, retro_ttru_1346, retro_ttru_1414, retro_ttru_149, retro_ttru_1762, retro_ttru_1816, retro_ttru_37, retro_ttru_375, retro_ttru_419, retro_ttru_650, retro_ttru_719, retro_ttru_872,
Vicugna pacos	ENSVPAG00000006867	6 retrocopies	retro_vpac_114, retro_vpac_164, retro_vpac_220, retro_vpac_354, retro_vpac_379, retro_vpac_518,