RetrogeneDB ID: retro_cfam_2004

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:38576187..38576805(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018340
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJA1
• Ensembl ID: ENSCAFG00000001818
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:HGNC Symbol;Acc:5229]

Sequence

>retro_cfam_2004
ATGGTGAAAGAAACCACTTACTATGATGTTTTGGGGGTCAAACACAATGCCACCCAGGAGGAATTGAAAAAGGCTTACAG
AAAACTGGCCTTGAAGTACCACCCTGATAAGAATCCAAATGAAGGAGAGAAGTTTAAACAGATTTCTCAAGCTTATGAAG
TGCTCTCTGATGCAAAGAAAGGGGAATTATATGACAAAGGAGGAGAACAGGCAATTAAAGAAGGTGGAGCTGGTGGTGGT
TTTGGCTCCCCCATGAACATCTTTGATATGTTTTTTGGAGGAGGAGGCAGGATGCAGAGAGAACGGAGAGGTAAAAATGT
TGTACATCAGCTCTCAGTAACCTTAGAAGATCTATATAATGGCGCAACAAGAAAACTAGCTCTGCAAAAGAATGTGATTT
GCGATAAATGTGAAGGCCGAGGTGGTAAGAAAGGAGCAGTCGAATGTTGTCCCAATTGCCGAGGTCCTGGAATGCAAATA
AGAATTCATCAGATAGGACCTGGAATGGTTCGGCAAATTCAATCTGTGTGCATGGAGTGCCAGGGCCATGGGGAACGGAT
CAGTCCTAAAGATAGATGTAAAAGCTGCAACGGAAGGAAGATAGTTCGAGAGAAGAAG

Alignment

ORF - retro_cfam_2004 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.57 %
• Parental protein coverage: 51.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGEQ
          MVKETTYYDVLGVK.NATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKK.ELYDKGGEQ
Retrocopy MVKETTYYDVLGVKHNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKGELYDKGGEQ

Parental  AIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
          AIKEGGAGGGFGSPM.IFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
Retrocopy AIKEGGAGGGFGSPMNIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR

Parental  GGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKK
          GGKKGAVECCPNCRG.GMQIRIHQIGPGMV.QIQSVCMECQGHGERISPKDRCKSCNGRKIVREKK
Retrocopy GGKKGAVECCPNCRGPGMQIRIHQIGPGMVRQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKK

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	0.13 RPM	39.44 RPM
SRP017611_brain	0.08 RPM	52.95 RPM
SRP017611_kidney	0.00 RPM	54.41 RPM
SRP017611_liver	0.00 RPM	20.30 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2004 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2004 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 169 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Bos taurus	ENSBTAG00000016265	6 retrocopies	retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004 , retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Choloepus hoffmanni	ENSCHOG00000000631	9 retrocopies	retro_chof_1760, retro_chof_186, retro_chof_2020, retro_chof_2541, retro_chof_2694, retro_chof_287, retro_chof_417, retro_chof_498, retro_chof_946,
Callithrix jacchus	ENSCJAG00000008022	10 retrocopies	retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus	ENSCPOG00000000462	6 retrocopies	retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Dasypus novemcinctus	ENSDNOG00000018342	3 retrocopies	retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Echinops telfairi	ENSETEG00000016984	6 retrocopies	retro_etel_1015, retro_etel_1454, retro_etel_1751, retro_etel_219, retro_etel_482, retro_etel_623,
Felis catus	ENSFCAG00000008729	5 retrocopies	retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Homo sapiens	ENSG00000086061	4 retrocopies	retro_hsap_2331, retro_hsap_2569, retro_hsap_3647, retro_hsap_4889,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Loxodonta africana	ENSLAFG00000001527	2 retrocopies	retro_lafr_1019, retro_lafr_936,
Myotis lucifugus	ENSMLUG00000016086	7 retrocopies	retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Macaca mulatta	ENSMMUG00000007740	6 retrocopies	retro_mmul_1313, retro_mmul_1802, retro_mmul_2477, retro_mmul_2482, retro_mmul_2625, retro_mmul_400,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mustela putorius furo	ENSMPUG00000004231	2 retrocopies	retro_mputfur_1543, retro_mputfur_487,
Mus musculus	ENSMUSG00000028410	3 retrocopies	retro_mmus_2561, retro_mmus_2982, retro_mmus_3507,
Nomascus leucogenys	ENSNLEG00000005268	4 retrocopies	retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Procavia capensis	ENSPCAG00000012273	2 retrocopies	retro_pcap_184, retro_pcap_220,
Pongo abelii	ENSPPYG00000019141	4 retrocopies	retro_pabe_1892, retro_pabe_2111, retro_pabe_2559, retro_pabe_2994,
Pan troglodytes	ENSPTRG00000020852	4 retrocopies	retro_ptro_1499, retro_ptro_1705, retro_ptro_177, retro_ptro_2472,
Pteropus vampyrus	ENSPVAG00000011470	1 retrocopy	retro_pvam_672,
Rattus norvegicus	ENSRNOG00000007029	2 retrocopies	retro_rnor_2208, retro_rnor_608,
Sorex araneus	ENSSARG00000001373	5 retrocopies	retro_sara_280, retro_sara_312, retro_sara_671, retro_sara_741, retro_sara_748,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Sus scrofa	ENSSSCG00000011000	2 retrocopies	retro_sscr_134, retro_sscr_984,
Ictidomys tridecemlineatus	ENSSTOG00000005200	4 retrocopies	retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Tupaia belangeri	ENSTBEG00000000596	23 retrocopies	retro_tbel_1281, retro_tbel_134, retro_tbel_1529, retro_tbel_1542, retro_tbel_2260, retro_tbel_2293, retro_tbel_2316, retro_tbel_2428, retro_tbel_2445, retro_tbel_2917, retro_tbel_2965, retro_tbel_2972, retro_tbel_329, retro_tbel_3345, retro_tbel_3353, retro_tbel_3692, retro_tbel_4014, retro_tbel_4223, retro_tbel_432, retro_tbel_591, retro_tbel_617, retro_tbel_634, retro_tbel_842,
Tarsius syrichta	ENSTSYG00000001329	4 retrocopies	retro_tsyr_110, retro_tsyr_1384, retro_tsyr_1921, retro_tsyr_57,
Tursiops truncatus	ENSTTRG00000007387	4 retrocopies	retro_ttru_1181, retro_ttru_1551, retro_ttru_567, retro_ttru_783,
Vicugna pacos	ENSVPAG00000001299	1 retrocopy	retro_vpac_367,