RetrogeneDB ID: retro_cfam_411

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:7592290..7593567(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC29A1
• Ensembl ID: ENSCAFG00000001981
• Aliases: SLC29A1, ENT1
• Description: Canis lupus familiaris solute carrier family 29 (nucleoside transporters), member 1 (SLC29A1), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001003367]

Sequence

>retro_cfam_411
CTGGTGGACATAGGCATTGGTATGACCAAAGCTGATCTCATAAATAACTTGGGAACCAGTACCAACTCTGGCACTGAAGC
ATTCATGGAGGCTCTTCAGGGTGGTGCAGACATCTCCATGATTGGACAGTTTGGTGTTGGCTTCTATTCTGCTTATCTGG
TGGCAGAGAAAGTGGTTGTTATCACAAAGCACAATGATGATGAACAGTATGCGTGGGAGTCTCCTGCTGGGGGCTCTTTC
ACTGTACGTGCAGACCATGGTGAGCCCATTGGCCAGGGTACCAAAATGATCCTTCATCTTAAAGAAGACCAAACAGAATA
TTTAGAGGAGACACATGTCAAAGAAGTGGTGAAGAAGCACTCCAAGTTCATAGGTTATCCCATCACCCTTTATTTGGAGA
AGGAATGAGAGAAAGAAATTAGTGATGATGAGGCAGAGGAGGAGAAAGGGGAGAAAGAGGAAGAAGATAAAGATGATGAG
GAGAACCCAAGACTGAAGATGTGGGTTCAGATGAGGAGGATGATAGTGAGAAGGACAAGAAAAAAAAAAAGACAAAGAAG
ATTAAGGAAAAATACATTGATCAAGAAGAACTGAACAAGACCAAGCCCGTTTGGACCAGAAACCCTGATGACATCACCCA
GGAGGAATATGGAGAGTTTTACAAGAGCCTTACTAATGACTGGGAAGATCACCTGGCAGTCAAACACTTCTCTGTAGAAG
GTCAGCTGGAATTCAGGGTATTGCTGATCGTCCCTCATTGGGCTCCTTTTGACCTCTTTGAGAACAAGAAGAAAAAGAAC
ATCAAACTCTATGTCCGCCATGTGTTCATCATGGACGGCTGTGATGAATTGATACCAGAGTATCTCAACTTCATCCGTGG
TGTGGTTGACTCTGAGGACCTGCCCCTGAACATCTCCCGAGAAATGCTCCAGCAAAGCAAAATCTTGAAGGTCATTTGCA
AAAATATAGTGAAGAAGTGCCTTGAGCTCTTCTCTGAATTGGCAGAAGACAAGGAGAACTATAAGAAATTCTGTGAGGCA
TTCTCTAAAAACCTAAAGCTTAGAATCCATGAAGATTCCACTAACCAGCGCTGCCTTTCTGAGCTGCTGTGTTACCACAC
TTCCCAGTCTGGAGATGAGATGACTTCTCTTTCAGAGTATGTGTCCCATATGAAGGAGACTCAGAAGTCCATCTATTACA
TCACCGGTAAGTGCAAAGAGCAGGTTGCCAACTCTGCTTTTGTGGAGCAAGTGCGGAAATGGGGCTTCGAGGTAGTA

Alignment

ORF - retro_cfam_411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.42 %
• Parental protein coverage: 58.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQY
          LVD.GIGMTKADLINNLGT...SGT.AFMEALQ.GADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQY
Retrocopy LVDIGIGMTKADLINNLGTSTNSGTEAFMEALQGGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQY

Parental  AWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEI
          AWES.AGGSFTVRADHGEPIG.GTK.ILHLKEDQTEYLEE..VKEVVKKHS.FIGYPITLYLEKE.EKEI
Retrocopy AWESPAGGSFTVRADHGEPIGQGTKMILHLKEDQTEYLEETHVKEVVKKHSKFIGYPITLYLEKE*EKEI

Parental  SDDEAEEEKGEKEEEDKDDEE-KPKIEDVGSDEEDDSGKDK-KKKTKKIKEKYIDQEELNKTKPIWTRNP
          SDDEAEEEKGEKEEEDKDDEE..PK.EDVGSDEEDDS.KDK....TKKIKEKYIDQEELNKTKP.WTRNP
Retrocopy SDDEAEEEKGEKEEEDKDDEE<EPKTEDVGSDEEDDSEKDKXXXXTKKIKEKYIDQEELNKTKPVWTRNP

Parental  DDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIM
          DDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFR.LL..P..APFDLFENKKKK.NIKLYVR.VFIM
Retrocopy DDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRVLLIVPHWAPFDLFENKKKK-NIKLYVRHVFIM

Parental  DSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAF
          D.CDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVI.KNIVKKCLELFSELAEDKENYKKF.EAF
Retrocopy DGCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVICKNIVKKCLELFSELAEDKENYKKFCEAF

Parental  SKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERV
          SKNLKL.IHEDSTN.R.LSELL.YHTSQSGDEMTSLSEYVS.MKETQKSIYYITG..KEQVANSAFVE.V
Retrocopy SKNLKLRIHEDSTNQRCLSELLCYHTSQSGDEMTSLSEYVSHMKETQKSIYYITGKCKEQVANSAFVEQV

Parental  RKRGFEVV
          RK.GFEVV
Retrocopy RKWGFEVV

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	0.13 RPM	792.27 RPM
SRP017611_brain	0.00 RPM	591.71 RPM
SRP017611_kidney	0.13 RPM	601.80 RPM
SRP017611_liver	0.00 RPM	460.46 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_411 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_411 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411 , retro_cfam_562, retro_cfam_881,
Canis familiaris	ENSCAFG00000018036	1 retrocopy	retro_cfam_1094,
Felis catus	ENSFCAG00000009764	1 retrocopy	retro_fcat_1177,
Gorilla gorilla	ENSGGOG00000008889	2 retrocopies	retro_ggor_1011, retro_ggor_701,
Macropus eugenii	ENSMEUG00000013735	1 retrocopy	retro_meug_1896,
Myotis lucifugus	ENSMLUG00000005239	2 retrocopies	retro_mluc_1604, retro_mluc_865,
Macaca mulatta	ENSMMUG00000022686	2 retrocopies	retro_mmul_1319, retro_mmul_1869,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Otolemur garnettii	ENSOGAG00000011961	1 retrocopy	retro_ogar_2574,
Pongo abelii	ENSPPYG00000016655	2 retrocopies	retro_pabe_2425, retro_pabe_415,
Rattus norvegicus	ENSRNOG00000019834	6 retrocopies	retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,
Tupaia belangeri	ENSTBEG00000014873	1 retrocopy	retro_tbel_1428,