RetrogeneDB ID: retro_cfam_1400

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:7829061..7829381(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2I
• Ensembl ID: ENSCAFG00000006601
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa [Source:HGNC Symbol;Acc:9196]

Sequence

>retro_cfam_1400
GGGACCTACTAGCTGGGTTTCATGGACAGTCAATTCTGCTAGAAATGTAAGAACATTCTTTATCCCAAGGAGGACAAGGA
GAACCCCATCTATTCTGTGTGTGCAAGAATTGTGATTACCAGCAGGAAGCTGACAACAGCTGCATCTATGTTGGCCTAAT
CACACAACAAGTAGACTAACCCAGATAGATCATCACTGGCAAGTCCCAGGACCCCTTGTGGGTAACAACTAAGCACCACA
TATGCCAAAAGTGAGGCCACAAGGAGGCAGTGTTCTTTGAGTTGCTCAGCGCCAGGGGCTGAGAGACCTGCAGGCCCTAT

Alignment

ORF - retro_cfam_1400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 85.6 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTYEPGFVGIRFCQECNNMLYPKEDKENRI-LLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIADVS
          GTY..GF....FC..C.N.LYPKEDKEN.I.L...C.NCDYQQEADNSCIYV..IT..VD....II...S
Retrocopy GTY*LGFMDSQFC*KCKNILYPKEDKENPI<LFCVCKNCDYQQEADNSCIYVGLITQQVD*PR*IITGKS

Parental  QDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLY
          QDP....T..H.CQK.GHKEAVFF...SAR.....R.Y
Retrocopy QDPLWVTTKHHICQK*GHKEAVFFELLSARG*ETCRPY

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	0.17 RPM	36.03 RPM
SRP017611_brain	0.00 RPM	11.59 RPM
SRP017611_kidney	0.00 RPM	29.45 RPM
SRP017611_liver	0.00 RPM	6.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1400 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1400 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006601	1 retrocopy	retro_cfam_1400 ,
Callithrix jacchus	ENSCJAG00000009671	1 retrocopy	retro_cjac_2777,
Dipodomys ordii	ENSDORG00000001852	2 retrocopies	retro_dord_264, retro_dord_555,
Monodelphis domestica	ENSMODG00000014172	1 retrocopy	retro_mdom_1465,
Mus musculus	ENSMUSG00000019738	1 retrocopy	retro_mmus_2287,
Oryctolagus cuniculus	ENSOCUG00000013044	2 retrocopies	retro_ocun_103, retro_ocun_1603,
Otolemur garnettii	ENSOGAG00000024254	1 retrocopy	retro_ogar_386,
Ochotona princeps	ENSOPRG00000001789	2 retrocopies	retro_opri_350, retro_opri_837,
Tursiops truncatus	ENSTTRG00000003919	1 retrocopy	retro_ttru_223,