RetrogeneDB ID: retro_cfam_1094

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:2736908..2738791(+)
• Located in intron of: ENSCAFG00000004479

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90AA1
• Ensembl ID: ENSCAFG00000018036
• Aliases: None
• Description: heat shock protein 90kDa alpha (cytosolic), class A member 1 [Source:HGNC Symbol;Acc:5253]

Sequence

>retro_cfam_1094
AATAACCTGGGTACCATCGCCAAGTCGGGGACCAAGGTGTTCATGGAGGCCTTGCAGGCTGGCGCAGATATTTCCATGAT
TGGCCAGTTTGGCGTCGGGTTTTATTCTGCCTACCTGGTGGCTGAGAAAGTGACGGTGATCACCAAGCATAACGACGACA
AGCAGTATGCCTGGGAGTCTTCTGCTGGAGGGTCGTTCACGGTTAGGACGGATACAGGTGAACCTATGGGTCGTGGAACA
AAGGTTATCCTGCATCTGAAGGAAGACCAGACTGAGTATCTGGAGGAGAGGAGGATAAAGGAGATTGTGAAGAAACATTC
TCAGTTCATTGGCTACCCCATTACTCTCTTTGTGGAGAAGGAACGTGATAAAGAAGTCAGTGACGATGAGGCTGAAGAAA
AGGAGGAGAAAGAGGAAGAAAAAGAAAAGGAAGAGAAAGAGTCTGATGACAAACCTGAAATAGAAGATGTTGGTTCGGAT
GAGGAGGAGGAGGAAAAGAAGGATGGAGACAAGAAGAAAAAGAAGAAGATCAAGGAGAAGTACATTGACCAGGAAGAGCT
GAACAAAACCAAGCCTATTTGGACCAGGAACCCTGACAACATCACCAACGAAGAATATGGGGAATTTTATAAGAGCTTGA
CCAATGACTGGGAAGATCACTTGGCAGTGAAGCATTTTTCAGTTGAAGGACAGCTGGAGTTCAGAGACCTTCTCTTTGTG
CCAAGACGTGCTCCCTTTGACCTATTCGAGAACAGAAAGAAAAAGAACAATATTAAGCTGTACGTTCGCAGAGTTTTCAT
TATGGATAACTGCGAGGAGCTGATCCCTGAGTATCTGAATTTCATTAGAGGTGTGGTGGACTCTGAAGATCTTCCTCTAA
ATATTTCCCGTGAGATGTTGCAGCAAAGCAAAATTTTGAAAGTTATCAGAAAAAATTTGGTCAAAAAGTGCTTGGAACTT
TTCACCGAACTGGCTGAAGACAGAACTACAAAAAGTTTTACAAGCAGTTCTCGAAAAACATCAAGCTGGGAATACATGAA
GATTCTCAAAATCGGAAGAAGCTGTCAGAGCTGTTACGATACTACACGTCGGCTTCTGGTGATGAGATGGTTTCTCTCAA
GGATTATTGCACTAGAATGAAGGAAAACCAGAAACACATCTATTACATCACAGGTGAGACCAAGGACCAGGTAGCAAACT
CTGCCTTTGTGGAGCGTCTTCGGAAGCATGGCCTGGAAGTGATCTATATGATCGAACCCATCGATGAGTACTGTGTCCAA
CAGCTTAAGGAATTTGAGGGGAAGACATTGGTGTCAGTCACCAAAGAGGGTTTGGAACTTCCAGAAGACGAAGAAGAGAA
GAAGAAACAGGAGGAGAAAAAAACAAAGTTTGAAAATCTGTGCAAGATCATGAAGGACATCTTGGAGAAAAAAGTAGAAA
AGGTGGTCGTGTCAAACCGATTGGTGACCTCCCCGTGCTGCATTGTCACAAGCACATATGGCTGGACGGCAAATATGGAG
AGAATCATGAAGGCCCAAGCCTTAAGAGACAACTCCACCATGGGTTACATGGCAGCAAAGAAGCACCTGGAGATAAACCC
TGACCACTCCATCATCGAGACCTTACGGCAGAAGGCAGAGGCCGACAAGAACGACAAGTCTGTGAAAGATCTGGTCATCC
TGCTCTATGAAACCGCTCTCCTGTCCTCCAGCTTCAGTCTGGAAGATCCCCAGACACATGCTAACAGGATCTACAGGATG
ATCAAGCTTGGGCTCGGTATCGACGAAGATGACCCCACAGCTGACGATAGCAGTGCTGCGGTGAGTGAGGAGATGCCGCC
CCTCTAAGGTGATGACGACACGTCACGCATGGAAGAAGTCGAT

Alignment

ORF - retro_cfam_1094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.63 %
• Parental protein coverage: 99.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRT
          NNLGTIAKSGTK.FMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDD.QYAWESSAGGSFTVRT
Retrocopy NNLGTIAKSGTKVFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDKQYAWESSAGGSFTVRT

Parental  DTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAEEKEEKEEE
          DTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEA.........
Retrocopy DTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAXXXXXXXXX

Parental  KEKKEKESDDKPEIEDVGSDEEEEEKKDGDKKKKKKIKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFY
          .......SDDKPEIEDVG...................KEKYIDQEELNKTKPIWTRNPD.ITNEEYGEFY
Retrocopy XXXXXXXSDDKPEIEDVGXXXXXXXXXXXXXXXXXXXKEKYIDQEELNKTKPIWTRNPDNITNEEYGEFY

Parental  KSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYLN
          KSLTNDWEDHLAVKHFSVEGQLEFR.LLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYLN
Retrocopy KSLTNDWEDHLAVKHFSVEGQLEFRDLLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYLN

Parental  FIRGVVDSEDLPLNISREMLQQSKILKVI-RKNLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHED
          FIRGVVDSEDLPLNISREMLQQSKILKVI..K....K.L..F........NYKKFY.QFSKNIKLGIHED
Retrocopy FIRGVVDSEDLPLNISREMLQQSKILKVI<QKKFGQKVLGTFHRTG*-RQNYKKFYKQFSKNIKLGIHED

Parental  SQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMI
          SQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMI
Retrocopy SQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMI

Parental  EPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRL
          EPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRL
Retrocopy EPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRL

Parental  VTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAKKHLEINPDHSIIETLRQKAEADKNDKSVKDL
          VTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAKKHLEINPDHSIIETLRQKAEADKNDKSVKDL
Retrocopy VTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAKKHLEINPDHSIIETLRQKAEADKNDKSVKDL

Parental  VILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGIDEDDPTADDSSAAVSEEMPPLEGDDDTSRMEEVD
          VILLYETALLSS.FSLEDPQTHANRIYRMIKLGLGIDEDDPTADDSSAAVSEEMPPL.GDDDTSRMEEVD
Retrocopy VILLYETALLSSSFSLEDPQTHANRIYRMIKLGLGIDEDDPTADDSSAAVSEEMPPL*GDDDTSRMEEVD

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	46.66 RPM	645.48 RPM
SRP017611_brain	129.25 RPM	925.48 RPM
SRP017611_kidney	42.40 RPM	282.44 RPM
SRP017611_liver	24.73 RPM	276.42 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

8 EST(s) were mapped to retro_cfam_1094 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BQ235722	2738013	2738440	100	427	0	427
DN373876	2738062	2738168	99.1	105	1	104
DN388207	2737920	2738385	99.6	463	2	461
DN443081	2737124	2737259	100	135	0	135
DT536386	2737165	2737336	99.5	170	1	169
DT539405	2738054	2738282	99.6	226	1	224
DT540102	2736981	2737426	99.8	442	1	441
GR894695	2737914	2738250	100	336	0	336

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1094 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1094 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Canis familiaris	ENSCAFG00000018036	1 retrocopy	retro_cfam_1094 ,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,