RetrogeneDB ID: retro_cfam_520

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:37199166..37200278(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BACE2
• Ensembl ID: ENSCAFG00000010157
• Aliases: None
• Description: beta-site APP-cleaving enzyme 2 [Source:HGNC Symbol;Acc:934]

Sequence

>retro_cfam_520
GCAGACAAGTCCAGTACGTACCGCTCCAAGGGCTTTGATGTCACTGCGAACTACACGCAAGGGAGCTGGACTGACATCGT
CGGGGAGGACTTTGTCACCATCCCCAAAGGCTTCAACAGCTCCTTCTTTGTCAACATTGCCACTATCTTTGAGTCCGAGA
ATTTCTTTCTGCCTGGTATCAAATGGAATGAGACACTTGAACTCGCATATGCTGCTCTGGCCAAGCCATCCAGTTCCCTG
GAGACTTTCTTTGATTCTCTGGCGGCGCAGGCGAAGATCCCCCAACGTCTTCTCCATGCAGATGTGGGGGGCGGGGCTGC
CCGTAGCTGGATCTGGTACCAACGGAGGTAGTCTTGTCCTGGGTGGAACTGAACCGAGTTTGTACAAAGGAGACATCTGG
TATACCCGTATTAAGGACGAGTGGTATTATCAGATAGAAATTCTGAAGTTGGAAATTGGAGGCCAGAGTCTGAATCTGGA
CTGCAGAGAGTATAACGCAGACAAGGCCATCGTGGATAGCGGTACCACGCTTCTGCGCCTGCCCCAGAAGGTGTTCAATG
TGGTGGTTGAAGCCGTGACCCGCACGTCTCTTGATTCCAGAATTCTCTGATGGTTTCTGGACTGGGTCCCAGCTGGCTTG
CTGGACGAATTCGGAGATACCTTGGTCTTACTTCCCTAAAATCTCCATCTACCTAGAGACGAGAACTCCAGCCAGTCATT
CGGCATAACCATCCTGCCTCAGCTGTACGTCCAGCCCATGATGGGGGCTGGCCTGAATTATAAATGTTACCGATTCGGCA
TCTCACCTTCCACGAACGCGCTGGTGATTGGTGCTACCGTGATGGAGGGCTTCTACGTGGTCTTCGACAGAGCTTGGAAG
AGGGTGGGCTTTGCAGCAAGCCCCTGTGCAGAAATTGCAGGTGCTCCAGTGTCTGAAATTTCTGGGCCTTTCTCGACAGA
CAACATAGCCAGCAACTGCGTCCCCGCCCTGTCTTTGAATGATCCCATTTTGTGGATCGTCTCCTATACTCTCTTGAGCG
TGTGTGGAATCATCCTTCTTCTCCTAATCATCCTGCTGCTACTTCCCTTCCCAGTGTCGGCACCTGCCCCGT

Alignment

ORF - retro_cfam_520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.44 %
• Parental protein coverage: 88.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ADRSSTYRSKGFDVTVKYTQGSWTGFVGEDFVTIPKGFNSSFLVNIATIFESENFFLPGIKWNGILGLAY
          AD.SSTYRSKGFDVT..YTQGSWT..VGEDFVTIPKGFNSSF.VNIATIFESENFFLPGIKWN..L.LAY
Retrocopy ADKSSTYRSKGFDVTANYTQGSWTDIVGEDFVTIPKGFNSSFFVNIATIFESENFFLPGIKWNETLELAY

Parental  AALAKPSSSLETFFDSLVAQAKIP-NVFSMQMCGAGLPVAGSGTNGGSLVLGGIEPSLYKGDIWYTPIKE
          AALAKPSSSLETFFDSL.AQAKIP.NVFSMQM.GAGLPVAGSGTNGGSLVLGG.EPSLYKGDIWYT.IK.
Retrocopy AALAKPSSSLETFFDSLAAQAKIP>NVFSMQMWGAGLPVAGSGTNGGSLVLGGTEPSLYKGDIWYTRIKD

Parental  EWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFNAVVEAVARTSL-IPEFSDGFWTG
          EWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFN.VVEAV.RTSL.IPEFSDGFWTG
Retrocopy EWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFNVVVEAVTRTSL>IPEFSDGFWTG

Parental  SQLACWTNSETPWSYFPKISIYL-RDENSSQSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIG
          SQLACWTNSE.PWSYFPKISIYL.RDENSSQSF.ITILPQLY.QPMMGAGLNY.CYRFGISPSTNALVIG
Retrocopy SQLACWTNSEIPWSYFPKISIYL<RDENSSQSFGITILPQLYVQPMMGAGLNYKCYRFGISPSTNALVIG

Parental  ATVMEGFYVVFDRARKRVGFAASPCAEIAGAPVSEISGPFSTDDIASNCVPALPLNEPILWIVSYTLMSV
          ATVMEGFYVVFDRA.KRVGFAASPCAEIAGAPVSEISGPFSTD.IASNCVPAL.LN.PILWIVSYTL.SV
Retrocopy ATVMEGFYVVFDRAWKRVGFAASPCAEIAGAPVSEISGPFSTDNIASNCVPALSLNDPILWIVSYTLLSV

Parental  CGIILLILIVLLLLPF-RCRHLPR
          CGIILL.LI.LLLLPF..CRHLPR
Retrocopy CGIILLLLIILLLLPF>QCRHLPR

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	0.04 RPM	7.69 RPM
SRP017611_brain	0.00 RPM	8.57 RPM
SRP017611_kidney	0.00 RPM	5.02 RPM
SRP017611_liver	0.00 RPM	4.13 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_520 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_520 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010157	1 retrocopy	retro_cfam_520 ,
Ciona intestinalis	ENSCING00000005258	1 retrocopy	retro_cint_2,
Ciona savignyi	ENSCSAVG00000008457	1 retrocopy	retro_csav_8,