RetrogeneDB ID: retro_cfam_1219

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:13072914..13073517(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000009888
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BID
• Ensembl ID: ENSCAFG00000016168
• Aliases: None
• Description: Canis lupus familiaris BH3 interacting domain death agonist (BID), mRNA. [Source:RefSeq mRNA;Acc:NM_001251938]

Sequence

>retro_cfam_1219
TCAGAGCCCCGCAAGGCTGCCCGTGCCATGGAATCTAAGGTGAGCAATGGCTCAGGCCCCCAGGATGAGCGTATCACCAA
TTTGCTAGTGTTTGGCTTCCTCCAAAACTGCTCCAACTATAACCTCCATGAAGAGTTGGAGCTGTTGGGCCATGAACTGC
CCGTGCCAGCTTACCTGAAGGAGGACCACGACAATGAGCTACAGACAGATGGCAACCGGTGCAGCTACTTCCTGGATGGT
GGGGTGAGAGATTCAGAAAGTCAAGAAGAAATCATCCAGGATATCGCCAGGCAGCTGGCACAAATAGGGGATAGGATGGA
TCACAGCATCCACCCAGGACTGGTGAATAACCTGGCAATGCAGTTTATGAATGTGAACCTATCGGAAGAAGACAGAAGGA
AGCATCTCGCTGCTGTGCTTGAGCAGGCCATGCAGACTTATCCTAAGGACACGGAAAAGGAGAAGACCATGCTGATGTTG
GCCATGCTGTTGGCCAAGAAGGTGGCCGACCACACCCCATCCTTGCTCTGTGACGTCTTTCACACAATAATGAACTTTAT
TAGCCAGAACCTGCTCACCTATGTGAGAAACTTAGTCAGAAAT

Alignment

ORF - retro_cfam_1219 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEPCKAAHAMESKVSNGSGPQDERITNLLVFGFLQNCSNYNFHEELELLGRELPVPAYLKEDYDDELQTD
          SEP.KAA.AMESKVSNGSGPQDERITNLLVFGFLQNCSNYN.HEELELLG.ELPVPAYLKED.D.ELQTD
Retrocopy SEPRKAARAMESKVSNGSGPQDERITNLLVFGFLQNCSNYNLHEELELLGHELPVPAYLKEDHDNELQTD

Parental  GNRCSYFLDGGARGLDSESQEEIIQDIARQLAQIGDRMDHSIHPGLVNNLAMQFMNVNLSEEDRRKHLAA
          GNRCSYFLDGG.R..DSESQEEIIQDIARQLAQIGDRMDHSIHPGLVNNLAMQFMNVNLSEEDRRKHLAA
Retrocopy GNRCSYFLDGGVR--DSESQEEIIQDIARQLAQIGDRMDHSIHPGLVNNLAMQFMNVNLSEEDRRKHLAA

Parental  ALEQAMQTYPKDMEKEKTMLMLAMLLAKKVADHTPSLLRDVFHTTVNFISQNLLTYVRNLVRN
          .LEQAMQTYPKD.EKEKTMLMLAMLLAKKVADHTPSLL.DVFHT..NFISQNLLTYVRNLVRN
Retrocopy VLEQAMQTYPKDTEKEKTMLMLAMLLAKKVADHTPSLLCDVFHTIMNFISQNLLTYVRNLVRN

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	0.08 RPM	31.42 RPM
SRP017611_brain	0.00 RPM	12.07 RPM
SRP017611_kidney	0.13 RPM	82.15 RPM
SRP017611_liver	0.07 RPM	20.81 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1219 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1219 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016168	1 retrocopy	retro_cfam_1219 ,
Felis catus	ENSFCAG00000011109	1 retrocopy	retro_fcat_1823,
Ictidomys tridecemlineatus	ENSSTOG00000020169	1 retrocopy	retro_itri_1393,