RetrogeneDB ID: retro_cfam_1625

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 38:6083261..6084322(+)
• Located in intron of: None

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_1625
ACAGTTGATGTACCAATGACAGACATGACATCTGTCTCGATGGGGCATAGCCAGTTGACCACCATTGATCAGTCAGAACT
AAGTTCTCAGCTTGGTTTGAGCTTAGGGGGTGGCACCATCCTGCCACCTGTCCAGTCACTCGAGGATCGTCTTTCAACCA
CCCCTTCACCTACTAGTTCACTTCCTGAGGATGGTGTTGAGGATTTCCGGAGGGAAGTTCCCAGCCAGAAGACAGTTGTG
GTGGAAGCAGGAAAAAAGCAGAAGGCCCCAAAGAAGAGAAAAAAGAAAAATCCTAATGAACCTCAGAAGCCAGTTTCAGC
ATATGCTTTATTTTTCGTGATACACAGGCTGCCATCAAGGGACAGAATCCCAATGCCACTTTTGGGGATGTTTCAAAAAT
TGTGGCCTCCGTGTGGGATAGTCTTGGAGAGGAGCAAAAACAAGTGTGTAAGAGGAAAACTGAAGCTGCTAAGAAAGAGT
ATCTGAAGGCTCTGGCTGCATATAAAAACAATCAAGAGTGTCTTGATTCCACAGTGCTACTGTGGAACCAGTAGATTTGG
ACCCAGTGCCACCTCCGCAGACGCCTTCTCCACCTCCTATGGCTACTGTTGACCCAGCATCTCCAGCACCAGCCACAACA
GAGCCCCTGCCCTGTCCCCTTCCATTATTGTTAACTCCACTCTTTCCTCCTATGTGGCAAACCAGGCATCTTCTGGGGCC
AGAGATCAACCCAACATCCCCAAGTTGATTATTACCAAACAGATGTTACCCTCTTCTATTACTATATCTCAAGGAGGGAT
AGTTACTGTTATCCCAGCCATAGTGGTGACCTCCCAGGGAATCCAACCAGGCCAAACCAGTACAGCCACTATCCAGCCCA
GTCAACAAGCCTAAATTGTCACTCGCTCAGTGTTGCAGGCAGCGGGAGAGGCCCTGCTTCTATGCAACTGCCTCCACCCC
GACTACAACCCCCTCCACTGAAACAGATGCTTCAGCCCCCCACTCAGCAGCAAGTGACCATTCTACAGCAGCCTCCCCGA
CTTCAGGCCTTGCAACAGCCA

Alignment

ORF - retro_cfam_1625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.17 %
• Parental protein coverage: 56.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TIDVPMADMTSGLMGHSQLTTIDQSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPTSSLHEDGVEDFR
          T.DVPM.DMTS..MGHSQLTTIDQSELSSQLGLSLGGGTILPP.QS.EDRLSTTPSPTSSL.EDGVEDFR
Retrocopy TVDVPMTDMTSVSMGHSQLTTIDQSELSSQLGLSLGGGTILPPVQSLEDRLSTTPSPTSSLPEDGVEDFR

Parental  RQVPSQKTVVVEAGKKQKAPKKRKKKDPNEPQKPVSAYALF-FRDTQAAIKGQNPNATFGEVSKIVASMW
          R.VPSQKTVVV................PNEPQKPVSAYALF.FRDTQAAIKGQNPNATFG.VSKIVAS.W
Retrocopy REVPSQKTVVVXXXXXXXXXXXXXXXXPNEPQKPVSAYALF<FRDTQAAIKGQNPNATFGDVSKIVASVW

Parental  DSLGEEQKQVYKRKTEAAKKEYLKALAAYKDNQEC-QATV-ETVELDPVPPSQTP---SPPPMATVDPAS
          DSLGEEQKQV.KRKTEAAKKEYLKALAAYK.NQEC...TV..TVE.....P...P...SPPPMATVDPAS
Retrocopy DSLGEEQKQVCKRKTEAAKKEYLKALAAYKNNQECLDSTV<ATVEPVDLDPVPPPQTPSPPPMATVDPAS

Parental  PAPATTEP-PALSPSIVVNSTLSSYVANQASSGAGGQPNITKLIITKQMLPSSITMSQGGMVTVIPATVV
          PAPATTEP.PALSPSI.VNSTLSSYVANQASSGA..QPNI.KLIITKQMLPSSIT.SQGG.VTVIPA.VV
Retrocopy PAPATTEP<PALSPSIIVNSTLSSYVANQASSGARDQPNIPKLIITKQMLPSSITISQGGIVTVIPAIVV

Parental  TSRGIQLGQTSTATIQPSQQAQIVTRSVLQAAAAA-AASMQLPPPRLQPPPLQQMPQPPTQQQVTILQQP
          TS.GIQ.GQTSTATIQPSQQA.IVTRSVLQAA..A..ASMQLPPPRLQPPPL.QM.QPPTQQQVTILQQP
Retrocopy TSQGIQPGQTSTATIQPSQQA*IVTRSVLQAAGEA<PASMQLPPPRLQPPPLKQMLQPPTQQQVTILQQP

Parental  PPLQAMQQP
          P.LQA.QQP
Retrocopy PRLQALQQP

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	65.77 RPM
SRP017611_brain	0.00 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_1625 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1625 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,