RetrogeneDB ID: retro_cfam_886

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:13872159..13872897(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004113
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GDI2
• Ensembl ID: ENSCAFG00000005223
• Aliases: GDI2, GDI-2
• Description: Canis lupus familiaris GDP dissociation inhibitor 2 (GDI2), mRNA. [Source:RefSeq mRNA;Acc:NM_001003184]

Sequence

>retro_cfam_886
CGTCCTTCATCTTACACCACTTCTAAAGTGGTGCTTTTACAGCGAGTCTCTGGCAAGATATGGCAAAAGCCCGTACCTCT
ACCCACTGTATGGCCTTGGGGAGCTGCCGCAGGGATTTGCAAGGCTAAGTGCTATTCATGGTGGCACCTACATGCTCAAT
AAACCCATTGAACAATCATTGTGCAAAATGGCAAAGTGATTGGTGTGAAATCTGAAGGAGAGGTTGCTCGCTGCAAGCAG
CTCATCTGTGACCCCAGCTACGTCAAAGACCGGGTAGAGAAGGTGGGCCAGGTCATCAGGGTTATCTGCATTCTCAGCCA
CCCCATCAAGAACACCAGTGACGCCAACTCCTGCCAGATCATCATCCCCCAGAACCAGGTCAATCGGAAGTCAGACGTCT
ACGTGTGCATGATCTCCTCTGCCCACAACGTGGCCGCGCAAGGGAAGTACATCGCCGTAGTGAGCACAACGGTGGAGACC
AAGGATCCCGAGAAGGAAATCAGACCAGCTTTGGAGCTTCTGGAACCAATTGAACGGAAATTCGTTAGCATCAGCGACGT
CCTTGTACCCAAAGACCTGGGGACGGAAAGCCAGATCTTTATTTCCCGCACGTACCATGCTACAACTCACTTTGAGACCA
CCTGTGACGATATTAAAAACATCTACAAGAGGATGACCGGCTCCGAGTTTGACTTTGAGGAAATGAAGCGCAGGAAGAAC
GACATCTACGGGGAAGAC

Alignment

ORF - retro_cfam_886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.53 %
• Parental protein coverage: 57.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QPCCETINRIKL-YSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEE-IIVQNGKVIG
          .P...T.....L.YSESLARYGKSPYLYPLYGLGELPQGFARLSAI.GGTYMLNKPIE..IIVQNGKVIG
Retrocopy RPSSYTTSKVVL>YSESLARYGKSPYLYPLYGLGELPQGFARLSAIHGGTYMLNKPIEQ<IIVQNGKVIG

Parental  VKSEGEVARCKQLICDPSYVKDRVEKVGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMI
          VKSEGEVARCKQLICDPSYVKDRVEKVGQVIRVICILSHPIKNT.DANSCQIIIPQNQVNRKSD.YVCMI
Retrocopy VKSEGEVARCKQLICDPSYVKDRVEKVGQVIRVICILSHPIKNTSDANSCQIIIPQNQVNRKSDVYVCMI

Parental  SSAHNVAAQGKYIAIVSTTVETKEPEKEIRPALELLEPIEQKFVSISDLLVPKDLGTESQIFISRTYDAT
          SSAHNVAAQGKYIA.VSTTVETK.PEKEIRPALELLEPIE.KFVSISD.LVPKDLGTESQIFISRTY.AT
Retrocopy SSAHNVAAQGKYIAVVSTTVETKDPEKEIRPALELLEPIERKFVSISDVLVPKDLGTESQIFISRTYHAT

Parental  THFETTCDDIKNIYKRMTGSEFDFEEMKRKKNDIYGED
          THFETTCDDIKNIYKRMTGSEFDFEEMKR.KNDIYGED
Retrocopy THFETTCDDIKNIYKRMTGSEFDFEEMKRRKNDIYGED

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	0.92 RPM	92.36 RPM
SRP017611_brain	0.08 RPM	98.92 RPM
SRP017611_kidney	0.13 RPM	219.05 RPM
SRP017611_liver	0.15 RPM	166.49 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_886 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_886 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196, retro_cfam_886 ,
Canis familiaris	ENSCAFG00000017406	1 retrocopy	retro_cfam_1873,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168, retro_cjac_3115,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971, retro_mmus_360,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,