RetrogeneDB ID: retro_cfam_360

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:46402545..46403311(+)
• Located in intron of: ENSCAFG00000002527

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1L2
• Ensembl ID: ENSCAFG00000006580
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]

Sequence

>retro_cfam_360
ATGTCTAAGTCAGAGTCTCCCAAAGAGCCCGAGCAGCTGCGGACGCTCTTCATCGGAGGTTTGAGCTTCGAAACGACCGA
TGAGAGTCTGAGGAGCCATTTTGAGCAATGGGGGACGCTTACGGACTGTGTGGTAATGAGAGACCCCAACACCAAGCGCT
CCAGAGGCTTTGGGTTCGTCACGTACGCCACCGTGGAGGAGGTGGACGCGGCCATGAACGCCCGGCCGCACAAGGTGGAC
TGAAGAGTCGTGGAACCAAAGAGGGCTGTCTCCCGAGAAGATTCTCAAAGACCCGGTGCCCACTTAACTGTGAAAAAGAT
TTTTTGTCGGTGGCATTAAAGAAGACACTGAAGAACATCATCTAAGAGATTATTTTGAACAGTATGGGAAAATTGAAGTG
ATTGAGATCATGACTGACCGAGGCAGTGGCAAAAAGAGAGGTTTCGCTTTTGTGACCTTTGACGACCACGACTCTGTAGA
CAAGATTGTCATTCAAAAATACCATACTGTGAATGGCCACAACTGTGAAGTAAGGAAAGCCCTATCGAAGCAAGAGATGG
CTAGTGCTTCGTCCAGCCAAAGAGGCCGAAGTGGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTTGGTGGGAAT
GACAACTTTGGTCGTGGAGGGAACTTCAGTGGTCGAGGTGGCTTCGGTGGCAGTCGAGGTGGTGGTGGATACGGTGGCAG
TGGGGATGGCTATAACGGATTTGGTAATGACGGAAGCAACTTTGGA

Alignment

ORF - retro_cfam_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.66 %
• Parental protein coverage: 68.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
          MSKSESPKEPEQLR.LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
Retrocopy MSKSESPKEPEQLRTLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA

Parental  AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKI-FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD
          AMNARPHKVD.RVVEPKRAVSREDSQRPGAHLTVKKI.FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD
Retrocopy AMNARPHKVD*RVVEPKRAVSREDSQRPGAHLTVKKI>FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD

Parental  RGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGG
          RGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGG
Retrocopy RGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGG

Parental  FGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGG
          FGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDG...G
Retrocopy FGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGSNFG

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	0.21 RPM	309.95 RPM
SRP017611_brain	0.08 RPM	85.58 RPM
SRP017611_kidney	0.33 RPM	187.02 RPM
SRP017611_liver	0.22 RPM	97.89 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_360 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000241	2 retrocopies	retro_cfam_408, retro_cfam_412,
Canis familiaris	ENSCAFG00000006580	16 retrocopies	retro_cfam_1080, retro_cfam_1081, retro_cfam_1170, retro_cfam_1323, retro_cfam_1616, retro_cfam_1844, retro_cfam_2017, retro_cfam_2128, retro_cfam_360 , retro_cfam_564, retro_cfam_702, retro_cfam_803, retro_cfam_839, retro_cfam_855, retro_cfam_892, retro_cfam_937,
Canis familiaris	ENSCAFG00000008940	1 retrocopy	retro_cfam_1086,
Canis familiaris	ENSCAFG00000013497	12 retrocopies	retro_cfam_1214, retro_cfam_1326, retro_cfam_1388, retro_cfam_1548, retro_cfam_1690, retro_cfam_1816, retro_cfam_265, retro_cfam_272, retro_cfam_400, retro_cfam_625, retro_cfam_65, retro_cfam_836,
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Macaca mulatta	ENSMMUG00000012989	5 retrocopies	retro_mmul_1031, retro_mmul_1427, retro_mmul_1726, retro_mmul_187, retro_mmul_1871,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,