RetrogeneDB ID: retro_cfam_861

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:12626652..12627543(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000030590
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSCAFG00000015125
• Aliases: None
• Description: karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]

Sequence

>retro_cfam_861
AACATGAAACCCATCTTTTGCAAGACAGCCATGAAACAAATGTTGCCTGTCCTGTCCCACCTCCTGCAGCACCAAGACAG
CGAGGTTCTCTCGGATACCTGCTGGGCCCTGTCCTACCTCACCAATGGCTGCAATGAGCGCATCGGCCAAGTGGTCAACA
CAGGGGTCCTGCCCAGGCTGGTCCAGCTTATGAGCAGCTCAGAGCTCAATGTCTTGACCCCTTCTCTCCGCACAATCGGG
AACATCGTCACAGGAACGGATTACCAGACCCAGATGGCCATTGACGCGGGCATGCTGAACGTGCTACCCCAACTCCTGAT
GCACCCCAAGTCCTCCATCCAGGAGGAGGCAGCTTGGGCCTTGAGCAATGTGGCTGCAGGGCCCTGCCAACATATCCAGC
GGCTGATCGCTTGCGGCATGCTGCCTCCCTTGGTGGCTCTGCTAAAAAATGGAGAATTTAAAGTCCAGAAAGAGGCTGTT
TGGACCGTGGCTAACTTCACAACTGGAGGCACCATAGACCAGTTGATCCACCTTGTCCACTCTGGAGTCCAGGAACCACT
GGTGAATCTGCTTACCATCCAAGACACCAAAATTGTTATCATCATCCTTGACGTTATCTCTTTTATCCTCCAGGTAGCAG
AGAAGCTTTCAGAGAAGGAAAATCTGTGTCTTCTGATAGAAAAAATTGGTGGCATTGATAAAATTGAGGCTTTTCAACTT
CATGAGAATCCTCAGTTTGCCCTGACTGCTTTGAACATTATCAAGAACCATTTTTGTGAGGGAGAAGAAAGTGGTGCAAC
ATTACCAGCCCTGGACCAAGATAATGAATTCTTAAACCGCTTAACAAAAAAACACCAAGGCCCCATGACTTCTAAACAAA
GGACCAAACCC

Alignment

ORF - retro_cfam_861 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.28 %
• Parental protein coverage: 56.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKNPYPCKTAVKQMLPVLSHLLQHQDSEVLSDTCWALSYLTDGCNERIGQVVNTGVLPRLVQLMSSSELN
          N..P..CKTA.KQMLPVLSHLLQHQDSEVLSDTCWALSYLT.GCNERIGQVVNTGVLPRLVQLMSSSELN
Retrocopy NMKPIFCKTAMKQMLPVLSHLLQHQDSEVLSDTCWALSYLTNGCNERIGQVVNTGVLPRLVQLMSSSELN

Parental  VLTPSLRTIGNIVTGTDYQTQMAIDAGMLNVLPQLLMHPKSSIQKEAAWALSNVAAGPCQHIQRLIACGM
          VLTPSLRTIGNIVTGTDYQTQMAIDAGMLNVLPQLLMHPKSSIQ.EAAWALSNVAAGPCQHIQRLIACGM
Retrocopy VLTPSLRTIGNIVTGTDYQTQMAIDAGMLNVLPQLLMHPKSSIQEEAAWALSNVAAGPCQHIQRLIACGM

Parental  LPPLVALLKNGEFKVQKEAVWIVANFTTGGTIDQLIHLVHSGVLEPLVNLLTIQDTKIVIIILDIISFIL
          LPPLVALLKNGEFKVQKEAVW.VANFTTGGTIDQLIHLVHSGV.EPLVNLLTIQDTKIVIIILD.ISFIL
Retrocopy LPPLVALLKNGEFKVQKEAVWTVANFTTGGTIDQLIHLVHSGVQEPLVNLLTIQDTKIVIIILDVISFIL

Parental  QAAEKLSEKENLCLLIEEIGGIDKIEALQLHENPQVALTALNIIENHFCEGEESGAILPALDQDNEFLNR
          Q.AEKLSEKENLCLLIE.IGGIDKIEA.QLHENPQ.ALTALNII.NHFCEGEESGA.LPALDQDNEFLNR
Retrocopy QVAEKLSEKENLCLLIEKIGGIDKIEAFQLHENPQFALTALNIIKNHFCEGEESGATLPALDQDNEFLNR

Parental  LTKKHQGPTTSKQRTKP
          LTKKHQGP.TSKQRTKP
Retrocopy LTKKHQGPMTSKQRTKP

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	0.42 RPM
SRP017611_brain	0.00 RPM	0.56 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.07 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_861 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_861 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Canis familiaris	ENSCAFG00000015125	2 retrocopies	retro_cfam_459, retro_cfam_861 ,
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Callithrix jacchus	ENSCJAG00000015943	1 retrocopy	retro_cjac_2964,
Equus caballus	ENSECAG00000000554	1 retrocopy	retro_ecab_981,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548,
Homo sapiens	ENSG00000185467	1 retrocopy	retro_hsap_3337,
Mus musculus	ENSMUSG00000038770	2 retrocopies	retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps	ENSOPRG00000015434	2 retrocopies	retro_opri_1101, retro_opri_118,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pan troglodytes	ENSPTRG00000019446	2 retrocopies	retro_ptro_102, retro_ptro_2142,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,