RetrogeneDB ID: retro_cfam_747

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:9968299..9969235(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000003639
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000016095
• Aliases: None
• Description: Glutamate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F1Q2N5]

Sequence

>retro_cfam_747
AGGTTTACCATGGAGCTGGCAAAGAAGGGCTTTATTGGTCCTGGCATTGATGTGCCTGCCCCAGACATGAGCACAGGTGA
GCGGGAGATGTCCTGGATTGCTGACACCTATGCCAGCACCATAGTGGACTATGATATTAATGTCCTTACCTGTGTTACTG
GTAAGCCCATCAGTCAGGGTGGGATCCATGGGCGGATCTCTGCAACTGGCCGGGAGTCTTCCATGGGATTGAAAATTTCA
TCAATGAAGCTTCTTACATGAGTATTTTAGGAATGACACCAGGGTTTGGAGATAAAACGTTTGTTGTTCAGGGATTTGGT
AACGTGGGCCTGCACTCTTTGAGATACTCACATCGTTTTGGTGCTAAATGTGTTGGTATTGGTGAATCTGATGGGAGCAT
ATGGAATCCAGATGGTATTGACCCAAAGGAACTGGAAGACTTCAAATTGCAACATGGATCAATCCTGGGCTTCCCCAAGG
CAAAGCCCTTATGAAGGGAGCATCTTGGAAGCTGATTGTGACATCCTGATCCCTGCTGCCAGCGAGAAGCAGCTGACCAA
GTCCAACACACCCAGAGTCAAAGCCAAGATCATTGCTGAGGGTGCCAATGGACCAACAACCCCAGAGGCCGATAAGATCT
TCCTGGAGAGGAACATCATGGTGATTCCAGACTTCTACTTGAATGCTGGAGGAGTGACAGTATCTTACTTTGAGTGGCTG
AAGAATCTGAATCATGTCAGCTATGGCCGTTTGACCTTCAAATATGAAAGGGATTCTAACTACCACTTGCTCATGTCTGT
TCAAGAGAGCTTGGAAAGGAAATTTGGAAGGCATGGTGGAACTATTCCCGTTGTGCCCACAGCAGAATTCCAAGACAGGA
TATCGGGTGCCTCCGAGAAGGACATCGTGCACTCTGGCCTAGCTTACACCATGGAA

Alignment

ORF - retro_cfam_747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.86 %
• Parental protein coverage: 64.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATG
          RFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTI..YDIN...CVTGKPISQGGIHGRISATG
Retrocopy RFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIVDYDINVLTCVTGKPISQGGIHGRISATG

Parental  R-GVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCVGVGESDGSIWNPDG
          R.GVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHS.RY.HRFGAKCVG.GESDGSIWNPDG
Retrocopy R<GVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSLRYSHRFGAKCVGIGESDGSIWNPDG

Parental  IDPKELEDFKLQHGSILGFPKAKP-YEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTP
          IDPKELEDFKLQHGSILGFPKAKP.YEGSILEADCDILIPAASEKQLTKSN.PRVKAKIIAEGANGPTTP
Retrocopy IDPKELEDFKLQHGSILGFPKAKP>YEGSILEADCDILIPAASEKQLTKSNTPRVKAKIIAEGANGPTTP

Parental  EADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKH
          EADKIFLERNIMVIPD.YLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFG.H
Retrocopy EADKIFLERNIMVIPDFYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGRH

Parental  GGTIPVVPTAEFQDRISGASEKDIVHSGLAYTME
          GGTIPVVPTAEFQDRISGASEKDIVHSGLAYTME
Retrocopy GGTIPVVPTAEFQDRISGASEKDIVHSGLAYTME

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	0.63 RPM	239.81 RPM
SRP017611_brain	0.32 RPM	205.15 RPM
SRP017611_kidney	0.00 RPM	272.54 RPM
SRP017611_liver	4.71 RPM	737.46 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_747 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_747 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747 ,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,