RetrogeneDB ID: retro_cfam_1698

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:43476660..43478454(-)
• Located in intron of: ENSCAFG00000017137

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOX4
• Ensembl ID: ENSCAFG00000005647
• Aliases: None
• Description: TOX high mobility group box family member 4 [Source:HGNC Symbol;Acc:20161]

Sequence

>retro_cfam_1698
CCCTTCCTGTCGGGGGCTGAGACATTCCATACACCAAGCTTGGGAGATGAGGAATTTGAAATCCCACCTATCTCCTTGGA
TTCTGACCCCTCACTGGTGTCTCGGATGTGGTTGGCCACTTTGGGGACCTGGAAGACCCCTCCTCCTCTCAGGATGGCAG
CTTTTCAGCCCAGTATGGGATCCAGACATTGGACATGCCTGTGGGCATGACCCATTGCTTACTGGAGCAGGGCAGGGGGG
CTCCTGAGTGGGGGCTTGACCATGGACTTGGACCATTCTATAGGAACTCAGTATAGTGCCAACCCACCTGTTACAATTGA
TGTACCAATGACAGACATGACATCTGGCTTGATGGAGCATAGCCGGTTGACCACCGCTGATCAGTCAGAACTGAGTTCTC
AACTTGGTTTGAGCTTAGGGGGTGGCACCATCCTGCCACCTGCCCAGTCACCTGAGGATCGTCTTTCAACCACCCCTACA
CCTACTAGTTCACTTCATGAGGATGGTATTGAGGATTTCCAGAAGCAAGTTCCCAGCCAGAAGGCCATTGTGGCGGAAGC
AGGAAAAAAGCATAAGGCCCCAAAGACGAAAAAAAAGAAAGATCCTAATAAACCTCAGAAGCCAGTTTCGGCATATGCTT
TATTCTTTCATGATACACAGGCTGCCCTCAAGGGACAAAATCCCAATGCCACTTTTGGGAAGGTTTCAAAAATTGTGGCC
TCCATGTGGGATAGTCTTGGAGAAGAGCAAAAACAGGTGTATAAGAGGAAAACTGAAGCTGCCAAGAAAGAGTATCTGAA
GGCTCTGGCTGCATATAAAGATAATCAAGAGTGTCAGGCCACTGTGGAAACGGTAGAATTGGATCCAGTGTCACCATGAC
AGACGCCTTCTCCACCTCCTATGGCTACTGTTGACCCAGCATCTCCAGCACCAGCCACAACAGAGCCCCCTGCCCTGTTC
CCTTCCATTGTCATTAACTCCACTCTTTCCTCCTATGTGGCAAACCAGGCATCTTCTGGGGCCGGAGGTCAGCCCAATAT
CACCAAGTTGATTACTACCAAACAGATGTTACCCTCTTCTATTACTATTTCTCTAGGAGGGATGGTTACCGTTATCCCAG
CCACAGTGGTGACCTCCCAGGGAATCCAAACCAGTACAGCCACTATCCAGCCCAGTCAACAAGCCCAAATTGTCACTCGC
TCAGTGTTGCAGGCGGCGGCAGCGGCCACTGCTTCTATGCAACTGCCTCCACCTCGACTACAACCCCCTCCACTGCAACA
GATGCCTCAGCCCTGCACTCAGCAGCATGTGACCATTCTGCAGCAGCCTCCCCCACTTCAGGCCATGCAACAGCCTCCAC
CCTAGAAAGTTCGAATCAATTTACAGCAACAGCCACCTCCTCTGCAGATCAAGATTGTACCTCCACCCACTCTCAAAATG
CAGACAACCTTAGTCCCACCAACTGTGGAAAGTAGTCCTGAGTAGCCTGTGAACAACAACCCTGAGGTCCATACAGTAGA
GGAAACCTCTCCTGAGATGATCTGTGAAATGATCACAGATGTAATTCCTGAGGTTGAATCTCCTTCTCAAATGGATGTTG
AATTGGTGAGTGGGTCTCCTGTGACACTCTCACCCCAGCCTCGATGTGTGAGGTCCAGCTGTGAGAACCCTTCCGTTGTG
AGTAAGGACTGGGACAATGAGTACTGCAGCAATGAATGTGTGGTGAAGCACTGCAGGGATGTCTTCTTGGCCTGGGTGGC
TTCTAGAAATTCAAACACAGTGATGTTTGTAGAG

Alignment

ORF - retro_cfam_1698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.22 %
• Parental protein coverage: 97.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PFLSGAETFHTPSLGDEEFEIPPISLDSDPSLA-VSDVVGHFDDLADPSSSQDGSFSAQYGVQTLDMPVG
          PFLSGAETFHTPSLGDEEFEIPPISLDSDPSL..VSDVVGHF.DL.DPSSSQDGSFSAQYG.QTLDMPVG
Retrocopy PFLSGAETFHTPSLGDEEFEIPPISLDSDPSLV<VSDVVGHFGDLEDPSSSQDGSFSAQYGIQTLDMPVG

Parental  MTHGLMEQG-GGLLSGGLTMDLDHSIGTQYSANPPVTIDVPMADMTSGLMGHSQLTTIDQSELSSQLGLS
          MTH.L.EQG.GGLLSGGLTMDLDHSIGTQYSANPPVTIDVPM.DMTSGLM.HS.LTT.DQSELSSQLGLS
Retrocopy MTHCLLEQG>GGLLSGGLTMDLDHSIGTQYSANPPVTIDVPMTDMTSGLMEHSRLTTADQSELSSQLGLS

Parental  LGGGTILPPAQSPEDRLSTTPSPTSSLHEDGVEDFRRQVPSQKTVVVEAGKKQKAPKKRKKKDPNEPQKP
          LGGGTILPPAQSPEDRLSTTP.PTSSLHEDG.EDF..QVPSQK..V.EA............KDPN.PQKP
Retrocopy LGGGTILPPAQSPEDRLSTTPTPTSSLHEDGIEDFQKQVPSQKAIVAEAXXXXXXXXXXXXKDPNKPQKP

Parental  VSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKTEAAKKEYLKALAAYKDNQEC
          VSAYALFF.DTQAA.KGQNPNATFG.VSKIVASMWDSLGEEQKQVYKRKTEAAKKEYLKALAAYKDNQEC
Retrocopy VSAYALFFHDTQAALKGQNPNATFGKVSKIVASMWDSLGEEQKQVYKRKTEAAKKEYLKALAAYKDNQEC

Parental  QATVETVELDPVPPSQTPSPPPMATVDPASPAPATTEPPALSPSIVVNSTLSSYVANQASSGAGGQPNIT
          QATVETVELDPV.P.QTPSPPPMATVDPASPAPATTEPPAL.PSIV.NSTLSSYVANQASSGAGGQPNIT
Retrocopy QATVETVELDPVSP*QTPSPPPMATVDPASPAPATTEPPALFPSIVINSTLSSYVANQASSGAGGQPNIT

Parental  KLIITKQMLPSSITMSQGGMVTVIPATVVTSRGIQLGQTSTATIQPSQQAQIVTRSVLQAAAAAAASMQL
          KLI.TKQMLPSSIT.S.GGMVTVIPATVVTS.GI...QTSTATIQPSQQAQIVTRSVLQAAAAA.ASMQL
Retrocopy KLITTKQMLPSSITISLGGMVTVIPATVVTSQGI---QTSTATIQPSQQAQIVTRSVLQAAAAATASMQL

Parental  PPPRLQPPPLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQQQPPPLQIKIVPPPTLKMQTTLV
          PPPRLQPPPLQQMPQP.TQQ.VTILQQPPPLQAMQQPPP.KVRINLQQQPPPLQIKIVPPPTLKMQTTLV
Retrocopy PPPRLQPPPLQQMPQPCTQQHVTILQQPPPLQAMQQPPP*KVRINLQQQPPPLQIKIVPPPTLKMQTTLV

Parental  PPTVESSPERPVNNSPEAHTVEETSPETICEMITDVVPEVESPSQMDVELVSGSPVTLSPQPRCVRSGCE
          PPTVESSPE.PVNN.PE.HTVEETSPE.ICEMITDV.PEVESPSQMDVELVSGSPVTLSPQPRCVRS.CE
Retrocopy PPTVESSPE*PVNNNPEVHTVEETSPEMICEMITDVIPEVESPSQMDVELVSGSPVTLSPQPRCVRSSCE

Parental  NPPVVSKDWDNEYCSNECVVKHCRDVFLAWVASRNSNTVVFVK
          NP.VVSKDWDNEYCSNECVVKHCRDVFLAWVASRNSNTV.FV.
Retrocopy NPSVVSKDWDNEYCSNECVVKHCRDVFLAWVASRNSNTVMFVE

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	0.00 RPM	65.77 RPM
SRP017611_brain	0.08 RPM	52.08 RPM
SRP017611_kidney	0.00 RPM	42.92 RPM
SRP017611_liver	0.00 RPM	24.15 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1698 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1698 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1698 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006261	1 retrocopy	retro_amel_858,
Canis familiaris	ENSCAFG00000005647	2 retrocopies	retro_cfam_1625, retro_cfam_1698 ,
Choloepus hoffmanni	ENSCHOG00000000714	2 retrocopies	retro_chof_2239, retro_chof_631,
Homo sapiens	ENSG00000092203	1 retrocopy	retro_hsap_2970,
Macropus eugenii	ENSMEUG00000010501	1 retrocopy	retro_meug_1384,
Mustela putorius furo	ENSMPUG00000000181	1 retrocopy	retro_mputfur_718,
Mus musculus	ENSMUSG00000016831	1 retrocopy	retro_mmus_11,
Nomascus leucogenys	ENSNLEG00000014556	1 retrocopy	retro_nleu_2027,
Pongo abelii	ENSPPYG00000005598	1 retrocopy	retro_pabe_2463,
Pan troglodytes	ENSPTRG00000006126	1 retrocopy	retro_ptro_2008,
Sus scrofa	ENSSSCG00000029203	1 retrocopy	retro_sscr_361,