RetrogeneDB ID: retro_cfam_1235

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:2351949..2352421(-)
• Located in intron of: ENSCAFG00000007233

Retrocopy information

• Ensembl ID: ENSCAFG00000029854
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARL2BP
• Ensembl ID: ENSCAFG00000008785
• Aliases: None
• Description: ADP-ribosylation factor-like 2 binding protein [Source:HGNC Symbol;Acc:17146]

Sequence

>retro_cfam_1235
GAAGTCTTGGGAAAAGAGAGCTTCTCATCGTCCATCTCTTCCATCTCTGAAGGCCAATTTGGTGCTGTGGTTGGCTCTAC
CCAGGACGTTGTCATGGATGCGGAGTTCCAGGTACTGCTGAGAAACCTCATGGACAGATACTACCAGGAGGTAGAGAATG
AACTCACCTACACACCCGCTTGTAATGAATACCTCTCTTTGGTAGAAAAGTACATTGAAGACAGCTGCTGGCGTGGATTC
CCAAATTCAACAAGGTGGCTTCCATAGCAACAGCACAGCACCGTGAAGATGAGGTGGCCAATGACCTATTCAACATGCTG
TTCACATTTACGGACTTTCTGGCATCCAGATGTTTCTGGACTATAGAGCAGAAAAAGAAGGCCAAGGGCTGGCCTTAAGC
AGTGGTTTAGGAGTGACTTCATTGTGCAAATCATCTCCCATGGCCCCTTCCCCGGAGCAATCTCTAGCACCA

Alignment

ORF - retro_cfam_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.76 %
• Parental protein coverage: 99.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DALEEESFALSFSSASDAEFDAVVGYLEDIIMDDEFQLLQRNFMDKYYQEFEDTEENKLTYTPIFNEYIS
          ..L..ESF..S.SS.S...F.AVVG...D..MD.EFQ.L.RN.MD.YYQE.....EN.LTYTP..NEY.S
Retrocopy EVLGKESFSSSISSISEGQFGAVVGSTQDVVMDAEFQVLLRNLMDRYYQEV----ENELTYTPACNEYLS

Parental  LVEKYIEE-QLLERIPGFNMAAFTTTLQHHKDEVAGDIFDMLLTFTDFLAFKEMFLDYRAEKEGR-GLDL
          LVEKYIE..QLL..IP.FN..A...T.QH..DEVA.D.F.ML.TFTDFLA....F......K....GL.L
Retrocopy LVEKYIED<QLLAWIPKFNKVASIATAQHREDEVANDLFNMLFTFTDFLA-SRCFWTIEQKKKAK<GLAL

Parental  SSGLVVTSLCKSSSV-PASQNDLRP
          SSGL.VTSLCKSS...P.....L.P
Retrocopy SSGLGVTSLCKSSPMAPSPEQSLAP

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	58.55 RPM
SRP017611_brain	0.00 RPM	60.10 RPM
SRP017611_kidney	0.00 RPM	40.68 RPM
SRP017611_liver	0.00 RPM	5.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1235 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 93 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004844	1 retrocopy	retro_btau_362,
Canis familiaris	ENSCAFG00000008785	3 retrocopies	retro_cfam_1026, retro_cfam_1235 , retro_cfam_1357,
Choloepus hoffmanni	ENSCHOG00000009016	16 retrocopies	retro_chof_1180, retro_chof_1220, retro_chof_1287, retro_chof_1526, retro_chof_1655, retro_chof_1677, retro_chof_1858, retro_chof_1904, retro_chof_2024, retro_chof_2189, retro_chof_2247, retro_chof_2646, retro_chof_2658, retro_chof_408, retro_chof_500, retro_chof_977,
Callithrix jacchus	ENSCJAG00000012116	9 retrocopies	retro_cjac_1766, retro_cjac_1920, retro_cjac_1928, retro_cjac_2548, retro_cjac_2580, retro_cjac_2698, retro_cjac_4074, retro_cjac_625, retro_cjac_689,
Dipodomys ordii	ENSDORG00000016342	2 retrocopies	retro_dord_227, retro_dord_579,
Equus caballus	ENSECAG00000016621	3 retrocopies	retro_ecab_307, retro_ecab_344, retro_ecab_754,
Felis catus	ENSFCAG00000002937	3 retrocopies	retro_fcat_400, retro_fcat_69, retro_fcat_974,
Loxodonta africana	ENSLAFG00000008633	3 retrocopies	retro_lafr_103, retro_lafr_228, retro_lafr_418,
Microcebus murinus	ENSMICG00000012467	6 retrocopies	retro_mmur_1066, retro_mmur_1385, retro_mmur_1444, retro_mmur_1515, retro_mmur_247, retro_mmur_499,
Macaca mulatta	ENSMMUG00000020352	7 retrocopies	retro_mmul_1260, retro_mmul_2037, retro_mmul_2055, retro_mmul_2059, retro_mmul_223, retro_mmul_2232, retro_mmul_2458,
Monodelphis domestica	ENSMODG00000013511	1 retrocopy	retro_mdom_1182,
Mustela putorius furo	ENSMPUG00000004306	2 retrocopies	retro_mputfur_1046, retro_mputfur_1369,
Nomascus leucogenys	ENSNLEG00000002803	7 retrocopies	retro_nleu_1050, retro_nleu_1939, retro_nleu_1946, retro_nleu_2114, retro_nleu_2332, retro_nleu_2428, retro_nleu_955,
Otolemur garnettii	ENSOGAG00000014535	9 retrocopies	retro_ogar_1448, retro_ogar_1476, retro_ogar_1657, retro_ogar_1658, retro_ogar_1919, retro_ogar_2427, retro_ogar_2475, retro_ogar_3184, retro_ogar_3352,
Procavia capensis	ENSPCAG00000005664	2 retrocopies	retro_pcap_110, retro_pcap_84,
Pteropus vampyrus	ENSPVAG00000001391	2 retrocopies	retro_pvam_507, retro_pvam_788,
Ictidomys tridecemlineatus	ENSSTOG00000010254	1 retrocopy	retro_itri_638,
Tupaia belangeri	ENSTBEG00000014441	1 retrocopy	retro_tbel_2991,
Tarsius syrichta	ENSTSYG00000004923	10 retrocopies	retro_tsyr_1003, retro_tsyr_1066, retro_tsyr_1205, retro_tsyr_1728, retro_tsyr_1755, retro_tsyr_1958, retro_tsyr_2144, retro_tsyr_28, retro_tsyr_298, retro_tsyr_351,
Tursiops truncatus	ENSTTRG00000012794	3 retrocopies	retro_ttru_1403, retro_ttru_325, retro_ttru_973,
Vicugna pacos	ENSVPAG00000005976	2 retrocopies	retro_vpac_242, retro_vpac_554,