RetrogeneDB ID: retro_cfam_321

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:78632036..78633008(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000001475
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3I
• Ensembl ID: ENSCAFG00000010674
• Aliases: EIF3I, EIF3S2
• Description: eukaryotic translation initiation factor 3, subunit I [Source:HGNC Symbol;Acc:3272]

Sequence

>retro_cfam_321
AAGCCCATCCTGCTGCAGGGCCAAGAACGATCCATTATGCAGATTAAGTACAACCGCGAGGGAGAGCTCCTCTTCACGGT
GGCCAAGGACCCTATTGTCAATGTGTGGTACTCCGTGAATGGTGAGAGGCTGGGCACTTACATGGGCCATAGTGGAGCTG
TGTGGTGTGTAGATGCTGACTGGGACACCAAACATGTCCTTAACCGGCTCAGCTGATAATAGCTGTCGTCTCTGGGACTG
TGAAACAGGGAAGCAGCTGGCTTTACTCAAGACCAATTCAGCTGTCAGGACGTGTGGCTTTGATTTTGGGGGCAACATCA
TCATGTTCTCCACGGACAAACAGATGGGCTACCAGTGCTTTGTGAGCTTCTTTGACCTGCGGGATCCAAGCCAAATTGAT
AACAATGAGCCCTACATTAAGATCCCTTGCAACAACTCCAAGATCACTAGTGCTGTTTGGGGACCCCTGGGGGAGTGCAT
CATCGCGGGTCATGAAGACAGAGAGCTCAACCAGTATAGCGCCAAGTCTGGAGAAGTACTGGTGAATGTTAAGGAGCACT
CCCAGCAGATCAATGATATCCAGTTATCCAGGGACATGACCATGTTTGTCACTGCTTCCAAGGACAACACAGCTAAGCTC
TTTGACTCCAAAACTCTTGAAGACCAGAAGACTTTCTGGACAGAACATCTAGTCAACTCAGCTGCCCTCTCTCCCAACTA
TGACCATGTGGTGCTGGGTGGTGGTCAGGAAGCCATGGATGTAACCACCACCTCTACCAGGATTGGCAAGTTTGAAGCCA
GATTCTTCCACTTGACCTTTGAAGAAGAGTTTGGAAGAGTCAAGGGTCACCTCGGACCCATCAACAGCGTTGCCTTCCAT
CCCAATGGCAAGAGCTATAGCAGCGGTGGTGAAGGTGGTTATGTCCACATCCACTAGTTCACCCACAGTACTTTGAATTT
GAGTTTGAGGCT

Alignment

ORF - retro_cfam_321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.25 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPILLQGHERSITQIKYNREGDLLFTVAKDPIVNVWYSVNGERLGTYMGHSGAVWCVDADWDTKHV-LTG
          KPILLQG.ERSI.QIKYNREG.LLFTVAKDPIVNVWYSVNGERLGTYMGHSGAVWCVDADWDTKHV.LTG
Retrocopy KPILLQGQERSIMQIKYNREGELLFTVAKDPIVNVWYSVNGERLGTYMGHSGAVWCVDADWDTKHV>LTG

Parental  SADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFVSFFDLRDPSQIDNNEPYM
          SADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFVSFFDLRDPSQIDNNEPY.
Retrocopy SADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFVSFFDLRDPSQIDNNEPYI

Parental  KIPCNDSKITSAVWGPLGECIIAGHEGGELNQYSAKSGEVLVNVKEHSRQINDIQLSRDMTMFVTASKDN
          KIPCN.SKITSAVWGPLGECIIAGHE..ELNQYSAKSGEVLVNVKEHS.QINDIQLSRDMTMFVTASKDN
Retrocopy KIPCNNSKITSAVWGPLGECIIAGHEDRELNQYSAKSGEVLVNVKEHSQQINDIQLSRDMTMFVTASKDN

Parental  TAKLFDSTTLEHQKTFRTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGR
          TAKLFDS.TLE.QKTF.TE..VNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGKFEARFFHL.FEEEFGR
Retrocopy TAKLFDSKTLEDQKTFWTEHLVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLTFEEEFGR

Parental  VKGHFGPINSVAFHPDGKSYSSGGEDGYVRIHYF-DPQYFEFEFEA
          VKGH.GPINSVAFHP.GKSYSSGGE.GYV.IH.F..PQYFEFEFEA
Retrocopy VKGHLGPINSVAFHPNGKSYSSGGEGGYVHIH*F<HPQYFEFEFEA

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	0.21 RPM	64.13 RPM
SRP017611_brain	0.71 RPM	50.97 RPM
SRP017611_kidney	1.06 RPM	131.88 RPM
SRP017611_liver	0.15 RPM	34.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_321 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_321 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_321 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010674	1 retrocopy	retro_cfam_321 ,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Homo sapiens	ENSG00000084623	2 retrocopies	retro_hsap_3888, retro_hsap_3894,
Gorilla gorilla	ENSGGOG00000001579	3 retrocopies	retro_ggor_2540, retro_ggor_2615, retro_ggor_2623,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129, retro_nleu_1135,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169, retro_pabe_3175,