RetrogeneDB ID: retro_cfam_1895

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:2629987..2631332(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000011119
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008640
• Aliases: None
• Description: None

Sequence

>retro_cfam_1895
CGTGAGTGTATCTCGACCCACGTTGGCCAGGCAGGTGTACAGATCGGCAATGCCTTCTGGGAGCTCTATTGCCTGGAACA
CGGCATTCAGCCCGATGGCCAGATGCCAAGTGACAAGACCATTAGGGGAGGAGATGACTCCTTCAACACCTTCTTCAGTG
AGACGGGCACTGGCAAGCATGTGCCCAGGGCGTGTTTGTAGACCTGGAGCCCACAGTCATTGATGAAGTTTGCAATGGCA
CCTACCGCCAGCTCCTCCACCCTGAGCAGCTCATCACAGGCAAGATGCTGCCAATAACTATGCCCAAGGGCACTACACCA
TTGGCAAGGAGATCATTGACCTTGTCTTGGACCAAATTCAGGAACTGGCTGGCCAGTGCACAGGTCTTCAGGGCTTCTTG
GTTTTCCACAGCTTTGGAGGGGGAACCGGTTCTGGGTTAATATCCCTGCTGATGGAACATCTCTCTGTCGATTATGGCAA
GAAGTCCAAGCTAGAGCTCTCCATCTACCCTCCCCCCCCAGGTGTCCACAGCTGTTTAGAGCCCTACAACTCCTTCCTCA
CCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACGACGAGGCCATCTATGACATCTGTCATAGAAAC
CTCGATATTGAGCACCCAACCTACACTAATCTAAACAGGCTGATAGGTCAGATTGTGTCCTCCATCACTGCTTCCCTCAG
ATTTGATGGAGCCCTGAATGTGGATCTGATGGAGTTCCAGACCAACCTGGTGCCCTATCCCTGCATCCACTTCCCTCTGG
CCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATGCATGCTTT
GAGCCAGCCAACCAGATGGTGAAACGTGACCCTCGCCATGGTAAATACATGGCTTGCTGCCTGTTGTACCATGGTGATGT
GGTTCCCAAAGATGTCAATGCTTCCATTGCCACCATCAAGACCAAGTGTACCATCCAGTTTGTGGACTGGTGCCCCACTG
GCTTCAAAGTAGGCATTAATTACCAGCCTCACACTGTGGTACCTGGTGGAGACCTGGCCAAACTACAGCAAGCTGTGTGC
ATGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGACTCACCTGGACCACAAGTTTGACCTGATGTATGCCAAGCATGC
CTTTGTTCACTGGTATGTGGGTGAAGGCATGGAGGAAGGAGAGTTTTCTGAGGCCCGTGAGGACATGGCTGCCCTGGAGA
AGGATTATGAGGAGGTTGGTGTGGATTCTGTTGAAGGAGAGGGTGAAGATGAAGGAGAAGAATAC

Alignment

ORF - retro_cfam_1895 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.94 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRA-VFVDL
          RECIS.HVGQAGVQIGNA.WELYCLEHGIQPDGQMPSDKTI.GGDDSFNTFFSETG.GKHVPRA.VFVDL
Retrocopy RECISTHVGQAGVQIGNAFWELYCLEHGIQPDGQMPSDKTIRGGDDSFNTFFSETGTGKHVPRA<VFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGK-EDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFH
          EPTVIDEV..GTYRQL.HPEQLITGK...A.N.YA.GHYTIGKEIIDLVLD.I..LA.QCTGLQGFLVFH
Retrocopy EPTVIDEVCNGTYRQLLHPEQLITGK<DAANN-YAQGHYTIGKEIIDLVLDQIQELAGQCTGLQGFLVFH

Parental  SFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAI
          SFGGGTGSG..SLLME.LSVDYGKKSKLE.SIYP.........EPYNS.LTTHTTLEHSDCAFMVD.EAI
Retrocopy SFGGGTGSGLISLLMEHLSVDYGKKSKLELSIYPXXXGVHSCLEPYNSFLTTHTTLEHSDCAFMVDDEAI

Parental  YDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAE
          YDIC.RNLDIE.PTYTNLNRLI.QIVSSITASLRFDGALNVDL.EFQTNLVPYP.IHFPLATYAPVISAE
Retrocopy YDICHRNLDIEHPTYTNLNRLIGQIVSSITASLRFDGALNVDLMEFQTNLVPYPCIHFPLATYAPVISAE

Parental  KAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPT
          KAYHEQLSVAEITNACFEPANQMVK.DPRHGKYMACCLLY.GDVVPKDVNA.IATIKTK..IQFVDWCPT
Retrocopy KAYHEQLSVAEITNACFEPANQMVKRDPRHGKYMACCLLYHGDVVPKDVNASIATIKTKCTIQFVDWCPT

Parental  GFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFS
          GFKVGINYQP.TVVPGGDLAK.Q.AVCMLSNTTAIAEAW..LDHKFDLMYAK.AFVHWYVGEGMEEGEFS
Retrocopy GFKVGINYQPHTVVPGGDLAKLQQAVCMLSNTTAIAEAWTHLDHKFDLMYAKHAFVHWYVGEGMEEGEFS

Parental  EAREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          EAREDMAALEKDYEEVGVDSVEGEGE.EGEEY
Retrocopy EAREDMAALEKDYEEVGVDSVEGEGEDEGEEY

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	2.39 RPM	465.89 RPM
SRP017611_brain	3.57 RPM	647.84 RPM
SRP017611_kidney	0.73 RPM	186.36 RPM
SRP017611_liver	0.29 RPM	50.18 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1895 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1895 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1895 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006872	4 retrocopies	retro_amel_1162, retro_amel_1367, retro_amel_1387, retro_amel_1895,
Canis familiaris	ENSCAFG00000005248	1 retrocopy	retro_cfam_1124,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895 , retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978,
Canis familiaris	ENSCAFG00000010412	1 retrocopy	retro_cfam_1418,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Cavia porcellus	ENSCPOG00000013016	1 retrocopy	retro_cpor_96,
Felis catus	ENSFCAG00000027011	1 retrocopy	retro_fcat_588,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Loxodonta africana	ENSLAFG00000010021	1 retrocopy	retro_lafr_326,
Microcebus murinus	ENSMICG00000017551	3 retrocopies	retro_mmur_144, retro_mmur_705, retro_mmur_885,
Myotis lucifugus	ENSMLUG00000002622	4 retrocopies	retro_mluc_154, retro_mluc_186, retro_mluc_234, retro_mluc_270,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Tupaia belangeri	ENSTBEG00000001671	1 retrocopy	retro_tbel_3700,
Tarsius syrichta	ENSTSYG00000013266	7 retrocopies	retro_tsyr_1014, retro_tsyr_1278, retro_tsyr_1281, retro_tsyr_1679, retro_tsyr_1834, retro_tsyr_243, retro_tsyr_6,
Tursiops truncatus	ENSTTRG00000004794	1 retrocopy	retro_ttru_407,