RetrogeneDB ID: retro_cfam_631

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:26785703..26786778(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002290
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008221
• Aliases: None
• Description: Fructose-bisphosphate aldolase [Source:UniProtKB/TrEMBL;Acc:F1PBT3]

Sequence

>retro_cfam_631
CAGGAACTGACCCGCAACACGCGCTGCCGACACCCCGCGCGGACCCGGGCGCAGAAGGAGCTTCCTGACGTCGCTCACCG
CATCGTGGCTCCGGGCAAGGGCGTCCTGGCTGCAGAGGAGTCCACTGGGAGCACCGCCAAGCGGCTGCAGTCCGTTGGCA
CCGAGGACACGGAGGAGAACCCGCGCTTCCACCGCCAGCTGCTGACCGCCGACCACCGCGTAAACCCCTGCGTTGGGGGT
GTCGTCCTCTTCCACGAGACACTGCACCAGAAGACCGACGACGGGCGTCCCTTCCCCCAAGTCACCAAATCCAAGGGTGG
TGCTGTAGGCATCAAGGTGGACAAAGGTGTGGTACCCCCGGCAGGAACAAATGGCGAGACAACCCCCCAAGGGCTGGCGG
GGCTGGCTGAGCGCTGTGCCCAGGACAGGAAGGAGGGGCCGACGTTGCCAAGTGGCGCTGTGTGCTGAAATTCGGGGACA
CACCCCCTCAGCCCTTGCCATCATGGAAAATGCCAACGTTCTGGCCCCTTATGCCAGCATCTGCCAGCAGAATGGCATCG
TGCCCATTGTGGAGCCTGAGGTCCTCCCCGATGGGGACCATGACTTGAAGGGCTGTCAGTATGTAACCGAGAGGGTGCTG
GCTGCTGTCTGCAGGGCTCTGAGTGACCGCCACATCTACCTGGAAGGCACTTTGCTGAAGCCCAATATGGTAACCCCAGG
CCATGTCTGCACCCATAGACATTCTCCTGAGGATATTGCCATGGCAACTGTCACAGCACTACCCCCCGCTGTTACTGGGA
TCACCTTCCTGTCAGGTGGCCAGAGTGAGGAGGAGGCATCCATCAATCTCAATGCCCTCAACAAGCCATGGGCCCTGACC
TTCTCCTATGGCCGAGCCCTACAGGCTTCTGCCCTGGAGGCCTGGGGTGGCAAGAAGGAGAACCTGAAGGCTGCCCAGGA
GGAGTATATGAAGCGAGCCCTGGCCAACAGCCTCGCCTGTCAAGGAAAGTACACCCCAAGTGGTCAGGCCGGGGCTGCAG
CCAGCGAGTCCCTCTTCATCCCTAACCAGGCCTAC

Alignment

ORF - retro_cfam_631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.11 %
• Parental protein coverage: 52.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KELTGNMPYQYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLL
          .ELT.N.....PA.T..QK.EL.D.AHRIVAPGKG.LAA.ESTGS.AKRLQS.GTE.TEEN.RF.RQLL.
Retrocopy QELTRNTRCRHPARTRAQK-ELPDVAHRIVAPGKGVLAAEESTGSTAKRLQSVGTEDTEENPRFHRQLL-

Parental  TADDRVNPCIGGVILFHETLYQKTDDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSER
          TAD.RVNPC.GGV.LFHETL.QKTDDGRPFPQV.KSKGG.VGIKVDKGVVP.AGTNGETT.QGL.GL.ER
Retrocopy TADHRVNPCVGGVVLFHETLHQKTDDGRPFPQVTKSKGGAVGIKVDKGVVPPAGTNGETTPQGLAGLAER

Parental  CAQYKKDG-ADFAKWRCVLKIGE-HTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRC
          CAQ..K.G.AD.AKWRCVLK.G..HTPSALAIMENANVLA.YASICQQNGIVPIVEPE.LPDGDHDLK.C
Retrocopy CAQDRKEG<ADVAKWRCVLKFGD<HTPSALAIMENANVLAPYASICQQNGIVPIVEPEVLPDGDHDLKGC

Parental  QYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTHKYSHEEIAMATVTALRRTVPPAVTGITFLS
          QYVTE.VLAAV..ALSD.HIYLEGTLLKPNMVTPGH.CTH..S.E.IAMATVTAL....PPAVTGITFLS
Retrocopy QYVTERVLAAVCRALSDRHIYLEGTLLKPNMVTPGHVCTHRHSPEDIAMATVTAL----PPAVTGITFLS

Parental  GGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYIKRALANSLACQGK
          .G...EE.......IN...L.KPWALTFSYGRALQASAL.AWGGKKENLKAAQEEY.KRALANSLACQGK
Retrocopy -GGQSEEEA----SINLNALNKPWALTFSYGRALQASALEAWGGKKENLKAAQEEYMKRALANSLACQGK

Parental  YTPSGQAGAAASESLFISNHAY
          YTPSGQAGAAASESLFI.N.AY
Retrocopy YTPSGQAGAAASESLFIPNQAY

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	445.94 RPM
SRP017611_brain	0.00 RPM	782.73 RPM
SRP017611_kidney	0.00 RPM	639.97 RPM
SRP017611_liver	0.00 RPM	74.04 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_631 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_631 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_631 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008221	2 retrocopies	retro_cfam_190, retro_cfam_631 ,
Callithrix jacchus	ENSCJAG00000006874	1 retrocopy	retro_cjac_1803,
Cavia porcellus	ENSCPOG00000007434	1 retrocopy	retro_cpor_951,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Homo sapiens	ENSG00000149925	1 retrocopy	retro_hsap_740,
Gorilla gorilla	ENSGGOG00000013979	1 retrocopy	retro_ggor_621,
Myotis lucifugus	ENSMLUG00000011210	3 retrocopies	retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta	ENSMMUG00000000983	1 retrocopy	retro_mmul_2596,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus	ENSMUSG00000030695	3 retrocopies	retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys	ENSNLEG00000002152	1 retrocopy	retro_nleu_133,
Oryctolagus cuniculus	ENSOCUG00000006329	1 retrocopy	retro_ocun_1550,
Ochotona princeps	ENSOPRG00000009760	1 retrocopy	retro_opri_914,
Pongo abelii	ENSPPYG00000007244	1 retrocopy	retro_pabe_636,
Pan troglodytes	ENSPTRG00000007983	1 retrocopy	retro_ptro_526,
Rattus norvegicus	ENSRNOG00000023647	7 retrocopies	retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,