RetrogeneDB ID: retro_cfam_144

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:119884345..119885434(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000031663
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000019160
• Aliases: None
• Description: None

Sequence

>retro_cfam_144
ATGTCCGTAGGAAAGAGCAGTGAGCCTTGGAGGCTGGGAGAAGACCCAGAAGAGGCCCAGGGCGTGGTGGATGCCCTACA
GACCAGGGCTGAGGAGGAGGAGGAGGAGCCGGGGGAGGTTTTATCTCCCCGAACTCCTCCCTCTCTGTTTTCCTCCTCCC
CTTACTTCTCCTTGTCTGGCGGGTGTTCTGGCGCCCAGGAGGAGGAGTCTGCTAATGAGGGGTCCCTAAGTCCTCTCCAG
TGCTCTCAGGGTGCTAACACCTCCCAGGGGGGCAGGGAAGCCAGTGCCCAGTTTGCTGGCCCCAACAGCCCAGAGGAGGT
GGGCTCAAGTGGCAGTGAAGGGGAGGAAGATGCTGACTCGTCCCCCTGTGGCGGGGCATCCCATGGCCTTGGCCAGCCCC
AGCCTGCTGTCCCCAGCAGCCCAGCGGAGGTGGGGTCAAACCCACCTGAACAGCAGGAAGATGAGCAGCCCCAGGGCAGT
TTCCACCTGAAGACGGCTGCCCTGGTGATATTCCTGCTCCTCAAGTATCGCACCAAGCAGCCCACCAGCAAGGCAGAGAT
GCTGGAGATCATCACCCCAGAATTCCAGGACAACTTCCCCGTCATCTTGCGCCAAGCGTCCATCTGCTTGCGGCTGGTCT
TTGGCCTAGACGTGATAGAAGTGGATCCCAGCGAGCACTACTACAACCTCAGCATCATCCTGGGCCTCACCTGGAATGGG
ACACTGAGTAGTCAGGGGGGCCTGCCCAAGACCAGCCTCCTGGTGCTGGTCCTGGGGTTGATCGTCCTGGCGGATGACTG
TGCACCCGAGGAGGAGGTGTGGGAGGCGATGGGGATCATGGGGGTATACGATGGCCAGGATCACATCCTCTTTGGGGCAC
CCAGGGACCTCCTCACCAATGTCTGGGTGCAGGAAGGCTACCTGGAGTGCCGGCAGGTGGCTGGCAGCAATCCTGCCCGT
AAGGAGTTCCTGTGGGGGCCCAGAGCCCTCCAGGAAACCAGCAAGTTGCAGGTCATGGACTACGTGCTCCAGCTTGGTAA
CAACAACCTTACTTACTCCCTGGCCCTGTGTGAACAGATTCTGAGATAA

Alignment

ORF - retro_cfam_144 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.77 %
• Parental protein coverage: 90.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STTEGSPSPLQSSQSAITSPYDGAARGLGQPQPAGPYSPALASPSLLAPMAQEDEQPQGTFHVKTAALVM
          S..E...S.......A..SP..GA..GLGQPQPA.P.SPA........P..QEDEQPQG.FH.KTAALV.
Retrocopy SPEEVGSSGSEGEEDADSSPCGGASHGLGQPQPAVPSSPAEVGSN--PPEQQEDEQPQGSFHLKTAALVI

Parental  FLLLKYRTKQPTSKAEMLEVITPAFQDDFLIILSEASICLRLVLGLDVTEVDPREDSYDLNIVLGLTWDG
          FLLLKYRTKQPTSKAEMLE.ITP.FQD.F..IL..ASICLRLV.GLDV.EVDP.E..Y.L.I.LGLTW.G
Retrocopy FLLLKYRTKQPTSKAEMLEIITPEFQDNFPVILRQASICLRLVFGLDVIEVDPSEHYYNLSIILGLTWNG

Parental  TLSGQGDLPKTSLLVLVLGLIVLEDDCAPEEEVWETLGVMGVYDGQEHIVYGEPRDLLTNVWVQEGYLEC
          TLS.QG.LPKTSLLVLVLGLIVL.DDCAPEEEVWE..G.MGVYDGQ.HI..G.PRDLLTNVWVQEGYLEC
Retrocopy TLSSQGGLPKTSLLVLVLGLIVLADDCAPEEEVWEAMGIMGVYDGQDHILFGAPRDLLTNVWVQEGYLEC

Parental  RPVAGSDPVRYEFLWGPRAYEETSKLQVMDYVFQVSSS
          R.VAGS.P.R.EFLWGPRA..ETSKLQVMDYV.Q....
Retrocopy RQVAGSNPARKEFLWGPRALQETSKLQVMDYVLQLGNN

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_144 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046143	2 retrocopies	retro_btau_1808, retro_btau_198,
Canis familiaris	ENSCAFG00000019160	1 retrocopy	retro_cfam_144 ,