RetrogeneDB ID: retro_cfam_1735

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:40899844..40900279(+)
• Located in intron of: ENSCAFG00000018209

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEB1
• Ensembl ID: ENSCAFG00000008152
• Aliases: None
• Description: transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) [Source:HGNC Symbol;Acc:11617]

Sequence

>retro_cfam_1735
GGTGGTGCGCGGGGAACTCGTGCAGTGGCTGCGGTGGCTGCAGGGCTGACGAGAAACTACTAAAGTTTCTGTCGAAGTAA
AGTAGAATTCCAGAAGAACATAATGGATGGAGAAGAGAAAACCTATGGTGGCTGTGAAGGCCCTGATGCCTTGTATGTCA
AATTGATGTCTTCGGATGGTCATGAATTTATTGTAAAAAGAGAACATGCACTAACATCCAGAACAATAAAAACCATGTTG
AGTGGCCCAGGTCAGTTTGCTGAGAACGAAACTAATGAAGTCAATTTTAGAGAGATCCCTTCACATGTGCTATCAAAAGT
ATGCGTGTACTTTACCTACAAGGTTCGCTACACTAACAGCTCCAAAGAGATTCCTGAATTCCCAACTGCACCTGAAATTG
CACTGAAACTGCTGACGGCTGCGAACTTCCTAGAT

Alignment

ORF - retro_cfam_1735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 97.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGARGAGAVAAVAAGLTRRKNFRCSCRSKVEFRKNIMDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKRE
          GGARG...........TR..N....CRSKVEF.KNIMDGEEKTYGGCEGPDA.YVKL.SSDGHEFIVKRE
Retrocopy GGARGTXXXXXXXXXXTR--NY*SFCRSKVEFQKNIMDGEEKTYGGCEGPDALYVKLMSSDGHEFIVKRE

Parental  HALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELL
          HALTS.TIK.MLSGPGQFAENETNEVNFREIPSHVLSKVC.YFTYKVRYTNSS.EIPEFP.APEIAL.LL
Retrocopy HALTSRTIKTMLSGPGQFAENETNEVNFREIPSHVLSKVCVYFTYKVRYTNSSKEIPEFPTAPEIALKLL

Parental  MAANFLD
          .AANFLD
Retrocopy TAANFLD

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	36.83 RPM
SRP017611_brain	0.00 RPM	17.86 RPM
SRP017611_kidney	0.00 RPM	26.48 RPM
SRP017611_liver	0.00 RPM	5.73 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1735 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1735 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008152	3 retrocopies	retro_cfam_1320, retro_cfam_1344, retro_cfam_1735 ,
Macropus eugenii	ENSMEUG00000015988	11 retrocopies	retro_meug_1209, retro_meug_1508, retro_meug_1531, retro_meug_1642, retro_meug_1740, retro_meug_1764, retro_meug_308, retro_meug_398, retro_meug_743, retro_meug_768, retro_meug_815,