RetrogeneDB ID: retro_cfam_459

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:32462414..32463199(-)
• Located in intron of: None

Retrocopy information

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

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_459
TGGGCCCTGTCCTACCTCACCAATAGCTGCAATGAGCGCATCGGCTAAGTGGTCAACTCAGGGGTCCTGCCCAGGCTGGT
CCAGCTTATGAGCAGCTCAGAGCTCAATGTCTTGACCCCCTCTCTCCGCACAATTGGAAACATCGTCACAGGAACGGATT
ATCAGACCCAGATGGCCGTTGACGCGGGCATGCTGAACGTGCTGCCCCAACTCCTGACACACCCCAAGTCTTCCATCCAG
AAGGAGGCAGCTTGGGCCTTGAGCATTGTGGCTGCAGGGTCCTGCCAACACATCCAGCGGCTGATCGCTTGCAGCATGCT
GCCTCCCTTGGTGGCTCTGCTTAAAAATGGAGAATTTAAAGTCCAGAAAGAGGCTGTTTGGACCGTGGCTAACTTCACAA
CTGGAGGCACCATAGACCAGTTGATCCACCTTGTCTATTCTGGAGTTCTGGAGCCATTGGTGAATCTGCTTACCATCCAA
GACACCAAAATTGTTATCACCATCCCTGACTTTCTCTCTTTTATCCTCCAGGCAGTAGAGAAGTTTTCAGAGAAGGAAAA
TCTGTGTCTTCTGATAGAAGAAATTGGTGGCATTGATAAAATTGAGGCTTTGCAAATTCATGAGAATCCTCAGGTTGCCC
TGACTGCTTTGAACATTATCAAGAGCCATTTTTGTGAGGGAGAAGAAAGTGTGCAATATTACCAGCCCTGGACCAAGATA
ATGAATTCTTAAACCGCTTAACAAAAAAGTACCAAGGCACCACAACTTCTAAAAGGACCAAACCC

Alignment

ORF - retro_cfam_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.53 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WALSYLTDGCNERIGQVVNTGVLPRLVQLMSSSELNVLTPSLRTIGNIVTGTDYQTQMAIDAGMLNVLPQ
          WALSYLT..CNERIG.VVN.GVLPRLVQLMSSSELNVLTPSLRTIGNIVTGTDYQTQMA.DAGMLNVLPQ
Retrocopy WALSYLTNSCNERIG*VVNSGVLPRLVQLMSSSELNVLTPSLRTIGNIVTGTDYQTQMAVDAGMLNVLPQ

Parental  LLMHPKSSIQKEAAWALSNVAAGPCQHIQRLIACGMLPPLVALLKNGEFKVQKEAVWIVANFTTGGTIDQ
          LL.HPKSSIQKEAAWALS.VAAG.CQHIQRLIAC.MLPPLVALLKNGEFKVQKEAVW.VANFTTGGTIDQ
Retrocopy LLTHPKSSIQKEAAWALSIVAAGSCQHIQRLIACSMLPPLVALLKNGEFKVQKEAVWTVANFTTGGTIDQ

Parental  LIHLVHSGVLEPLVNLLTIQDTKIVIIILDIISFILQAAEKLSEKENLCLLIEEIGGIDKIEALQLHENP
          LIHLV.SGVLEPLVNLLTIQDTKIVI.I.D..SFILQA.EK.SEKENLCLLIEEIGGIDKIEALQ.HENP
Retrocopy LIHLVYSGVLEPLVNLLTIQDTKIVITIPDFLSFILQAVEKFSEKENLCLLIEEIGGIDKIEALQIHENP

Parental  QVALTALNIIENHFCEGEES-GAILPALDQDNEFLNRLTKKHQGPTTSKQRTKP
          QVALTALNII..HFCEGEES..AILPALDQDNEFLNRLTKK.QG.TTSK.RTKP
Retrocopy QVALTALNIIKSHFCEGEES<CAILPALDQDNEFLNRLTKKYQGTTTSK-RTKP

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	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_459 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_459 has 0 orthologous retrocopies within eutheria group .

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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,