RetrogeneDB ID: retro_cfam_198

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:89337857..89339849(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018271
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000003595
• Aliases: None
• Description: None

Sequence

>retro_cfam_198
ATGTCTCGGGACCCGTTCCGGAGCCGGGGCGGCGGTGGCTTCCACCGGCGCGGAGGAGGCCGCGGCCGCGGTGGCCTCCA
CGACTTCCGCTCCCCGCCGCCCGGCATGGGCCTCAATCAGAGCCGGGGACCCATGGGGCCCGGCCCGGGCCAGGGCGGCC
CCAAGCCCCCGATCCCGCCACCACCTCCGTACCAGCCGCCGCCGCCGCCACAGGCCCCGTCCAAGCCCGTCGGTGCTCAG
GGACCCTGGCCGGCTCCGGGAGAGGGCAGCGCTCCGCCGGCCTCCGGCTCGGCACGGCCCGCCACTCCTCCGACGTCGGG
GGCCCCTGCGGGCCCCGGACCCACCCCGCGGCCGCCGCCGCTGCCCGCAGTCACCTCGGCGCCCCCAGGGGCGCCCCAGA
CCGCGCCGCCGTGCGGCGGGGTCCCCACCACCCCGCCCCAGGCCGGGGACCCGCCGCCTCCACCTGCAGGGGGCCCGGGC
CCCGGACCTAAACAGGGCCCAGGCCCCGGAGGCCCGAAAGGCGGCACAATGCCAGGCGGCCCGGGGCTAAGGACTCCCGG
CGGCCTCCCCACGCCATGGCACCGGGGTGGCGGCGCGGGAGCCCCGCGAGGGGGCAAGCGCCACCCGCCCTACGGCCAGC
AGCACCGGCAGGGGCCCCCGCCCCGCGGCCGCAGCGAGGAGGAGGTGCACTCGGAGGGGTTCAAAGCCAGCCTGTCCCTC
CTGAGGAGGCCTGGAGAGAAAACTTACACTCAGCGCTGTCGGTTGTTTGTTGGGAATCTGCCTGCTGATATCACAGAGGA
TGAACTCAAAAGACTCTTTGCTAAATACGGAGAACCAGGAGAAGTTTTTATCAACAAAGGCAAAGGATTCGGGCTTATTA
AACTTGAATCTAGGGCACTGGCTGAAATTGCCAAAGCTGAACTCGATGATACACCCATGAGGGGTAGGCAGCTTCGGGTT
CGCTTTGCCACACATCCTGCTGCCCTGTCCGTGCGAAATCTTTCACCTTATGTTTCCAATGAACTCTTGGAAGAAGCCTT
TAGCCAGTTTGGTCCTATTGAGAGGGCTGTTGTAATTGTGGATGATCGTGGGAGATCTACAGGGAAAGGCATTGTTGAAT
TTGCTTCTAAACCAGCGGCAAGAAAAGCATTTGAAAGATGCGGCAAAGGTGTTTTCTTACTGACAACAATGCCTCGTCCA
GTCATTGTGGAACCACTTGAACAATTAGATGATGAAGATGGCCTTCCTGAAAAACTTGCACAGAGGAATCCAATGTACCA
AAATGAGAGAGAAATGCCTCCTCGTTTTGCCCAGTATGGCACACTTGAGTATGAATATTCTCAGCGATGGAAGTCCCTGG
ATGAAATGGAAAAACAGCAAAGGGAACAAGTTGAAAAAATCATGAAAGATGCGAAAGACAAATTGGAAAATGAAATGGAA
GATGCCTATCATGAGCATCGGGCAAATCTTTTGCGTCAAAATCTGATGAGGTGCCAGGAAGAATTAAGACGCATGGAAGA
ACTTCACAATCAAGAAATGCAGAAACGCAAAGAAATGCAACTAAAGCAAGAAGAAGAACGGCGTAGAAGGGAAGAAGAGA
TGATGATTCGGCAGCGTGAGATGGAAGAACAAATGAGACGCCAAAGAGAGGAAAGTTATAGCCGGATGGGCTACATGGAT
CCAAGAGAAAGAGACATGAGAATGGGTGGTGGAAGAACAATGAACATGGGAGATCCCTATGGTTCAGGAGGCCAGAAATT
TCCACCTCAAGGTGGTGGTGGTGGCATAGGTTATGAAGCTAATCCTGGAGTCCCACCAGCAACCATGAGCGGTTCCATGA
TGGGAAGCGACATGCCTACTGAGCACTTTGGGCAGGGAGGTGTGGAACCTGTAGGTGGACAGGGTCCTAGAGGAATGGGG
CCTGGGACTCCAGCAGGATATGGTAGAGGGAGAGAAGAGTATAAAGGCCCAAACAAAAAGCCCCAATTTTAG

Alignment

ORF - retro_cfam_198 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRDRFRSRGGGGGGFHRRGGGGGRGGLHDFRSPPPGMGLNQNRGPMGPGPGQGGPK---PPIPPLQPVG
          MSRD.FRSRGGGG..FHRRGGG.GRGGLHDFRSPPPGMGLNQ.RGPMGPGPGQGGPK...PP.PP.QP..
Retrocopy MSRDPFRSRGGGG--FHRRGGGRGRGGLHDFRSPPPGMGLNQSRGPMGPGPGQGGPKPPIPPPPPYQPPP

Parental  P-QGPG-PAPGVGSAP-PASGSAPPATPPTSGAPAGPGPTPTPP-PAVTSAPPGAPPPAPPSSGVPTTPP
          P.Q.P..P....G..P.P..GSAPPA....S..PA.P.....P..P..T..PP..P.......G.P.T.P
Retrocopy PPQAPSKPVGAQGPWPAPGEGSAPPASG--SARPATPPTSGAPAGPGPTPRPPPLPAVTSAPPGAPQTAP

Parental  QAGGPP--PPPAGGPGPGPKQGPGPGGPKGGKMPGGPKPG---GGPGLSTPGGHPKPPHRGGGE--PRGG
          ..GG.P..PP.AG.P.P.P..GPGPG.PK.G..PGGPK.G...GGPGL.TPGG.P.P.HRGGG...PRGG
Retrocopy PCGGVPTTPPQAGDPPPPPAGGPGPG-PKQGPGPGGPKGGTMPGGPGLRTPGGLPTPWHRGGGAGAPRGG

Parental  RQHHPPYHQQHHQGPPPGGPVGRSEEKISDSEGFKANLSLLRRPGEKTYTQRCRLFVGNLPADITEDEFK
          ..H.PPY.QQH.QGPP...P.GRSEE....SEGFKA.LSLLRRPGEKTYTQRCRLFVGNLPADITEDE.K
Retrocopy KRH-PPYGQQHRQGPP---PRGRSEEEVH-SEGFKASLSLLRRPGEKTYTQRCRLFVGNLPADITEDELK

Parental  RLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPMRGRQLRVRFATHAAALSVRNLSPYVSN
          RLFAKYGEPGEVFINKGKGFG.IKLESRALAEIAKAELDDTPMRGRQLRVRFATH.AALSVRNLSPYVSN
Retrocopy RLFAKYGEPGEVFINKGKGFGLIKLESRALAEIAKAELDDTPMRGRQLRVRFATHPAALSVRNLSPYVSN

Parental  ELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLD
          ELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFERC..GVFLLTT.PRPVIVEPLEQLD
Retrocopy ELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFERCGKGVFLLTTMPRPVIVEPLEQLD

Parental  DEDGLPEKLAQKNPMYQKERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAKDKLESEME
          DEDGLPEKLAQ.NPMYQ.ERE.PPRFAQ.GT.EYEYSQRWKSLDEMEKQQREQVEK.MKDAKDKLE.EME
Retrocopy DEDGLPEKLAQRNPMYQNEREMPPRFAQYGTLEYEYSQRWKSLDEMEKQQREQVEKIMKDAKDKLENEME

Parental  DAYHEHQANLLRQDLMRRQEELRRMEELHNQEMQKRKEMQLRQEEERRRREEEMMIRQREMEEQMRRQRE
          DAYHEH.ANLLRQ.LMR.QEELRRMEELHNQEMQKRKEMQL.QEEERRRREEEMMIRQREMEEQMRRQRE
Retrocopy DAYHEHRANLLRQNLMRCQEELRRMEELHNQEMQKRKEMQLKQEEERRRREEEMMIRQREMEEQMRRQRE

Parental  ESYSRMGYMDPRERDMRMGGGGAMNMGDPYGSGGQKFPPLGGGGGIGYEANPGVPPATMSGSMMGSDMRT
          ESYSRMGYMDPRERDMRMGGG..MNMGDPYGSGGQKFPP.GGGGGIGYEANPGVPPATMSGSMMGSDM.T
Retrocopy ESYSRMGYMDPRERDMRMGGGRTMNMGDPYGSGGQKFPPQGGGGGIGYEANPGVPPATMSGSMMGSDMPT

Parental  ERFGQGGAGPVGGQGPRGMGPGTPAGYGRGREEYEGPNKKPRF
          E.FGQGG..PVGGQGPRGMGPGTPAGYGRGREEY.GPNKKP.F
Retrocopy EHFGQGGVEPVGGQGPRGMGPGTPAGYGRGREEYKGPNKKPQF

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	0.80 RPM	189.75 RPM
SRP017611_brain	0.24 RPM	74.23 RPM
SRP017611_kidney	0.26 RPM	62.80 RPM
SRP017611_liver	0.07 RPM	36.33 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_198 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_198 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003595	1 retrocopy	retro_cfam_198 ,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98,
Callithrix jacchus	ENSCJAG00000001431	4 retrocopies	retro_cjac_1073, retro_cjac_2542, retro_cjac_2697, retro_cjac_486,
Felis catus	ENSFCAG00000031287	1 retrocopy	retro_fcat_1989,
Gasterosteus aculeatus	ENSGACG00000002034	1 retrocopy	retro_gacu_13,
Gadus morhua	ENSGMOG00000011950	1 retrocopy	retro_gmor_20,
Macropus eugenii	ENSMEUG00000014082	1 retrocopy	retro_meug_164,
Oryctolagus cuniculus	ENSOCUG00000001877	1 retrocopy	retro_ocun_1834,
Oreochromis niloticus	ENSONIG00000017737	1 retrocopy	retro_onil_21,
Sarcophilus harrisii	ENSSHAG00000016107	1 retrocopy	retro_shar_36,
Tetraodon nigroviridis	ENSTNIG00000011331	1 retrocopy	retro_tnig_32,
Takifugu rubripes	ENSTRUG00000003783	1 retrocopy	retro_trub_8,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,