RetrogeneDB ID: retro_cfam_1705

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:62098274..62099049(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000031509
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SAE1
• Ensembl ID: ENSCAFG00000004180
• Aliases: None
• Description: SUMO1 activating enzyme subunit 1 [Source:HGNC Symbol;Acc:30660]

Sequence

>retro_cfam_1705
GCTGCCAGGGTGCTCCTTGTTGGCATGAAAGGACTTGGGGCTAACTTTGCTAAGAATCTCATTCTGGCAGGAGTGAAAGG
ACTGACCATGTTGGATCCTAAACAGGTATCTCCAGAAGACCCTGAAGCTCAGTTCCTTATCCATACTGGATCTGTTGGCT
GTAACAAGGGCTGAAGCCTCTTTGGAACAAGCCCAAAATCTCAACCCAGTGGTGGATATGAAGGTGGACACCCAGAATAC
AGAGAAGAAACCTGAGTCATTTTTCACTCTGTTTGACATGACCTGTCTGACTTGCTGCTCCAGGGATGTCAAAGTCAAAG
TTGACCAGATCTGTCACAAAAATAATATCAAGTTTTTTAGAGGAGATGATGTTTTTGGCTACAATGGGTATACATTTGCC
AATCTTGGAGAGCATGAATTTGTAGAGGAGAAAACCAAAGTTGCCAAAGTTAGCCAATGGGTAGAAGAAGATGGACCTGA
TACCAAGAGCAAAACTTGATTCATCTGAAACAACTAGGTCAAAAAGAAGGTGGTCTTTTGCTCTATTAAGGAAGGGCCAC
AAGTGGACTGGAGCAGTGATAAAGCAAAAGTAGCTCTGAAGTTCACAACTTTGGGTTACTTTCTCCTTCAAGAGCTCCTG
AAGTTCTGCACAAGTAAAGGAAGAGATACTAGTTCTGTTACCTTTGGGGGAGATTCTGAGTTGTTGCTCCAGGTTTGAAA
CAACATGCTTGACTCCCTGGTTGTTAGTCCTGACCTGCTCCCTGAAGACACTATT

Alignment

ORF - retro_cfam_1705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 74.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASRVLLVGMKGLGAEIAKNLILAGVKGLTMLDPEQVSPEDPGAQFLVRTGSVGRN-RAEASLERAQNLNP
          A.RVLLVGMKGLGA..AKNLILAGVKGLTMLDP.QVSPEDP.AQFL..TGSVG.N.RAEASLE.AQNLNP
Retrocopy AARVLLVGMKGLGANFAKNLILAGVKGLTMLDPKQVSPEDPEAQFLIHTGSVGCN>RAEASLEQAQNLNP

Parental  MVDVKVDIENIEKKPESFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGD-VFGYHGYTFANLGEHE
          .VD.KVD..N.EKKPESFFT.FD..CLTCCSRDV.VKVDQICHKN.IKFF.GD.VFGY.GYTFANLGEHE
Retrocopy VVDMKVDTQNTEKKPESFFTLFDMTCLTCCSRDVKVKVDQICHKNNIKFFRGDDVFGYNGYTFANLGEHE

Parental  FVEEKTKVA-KVSQGVEDGPDTKRAKLDSSETTM-VKKKVVFCSIKEALEVDWSSDKAKAALKRTTSDYF
          FVEEKTKVA.K...G........RAKLDSSETT..VKKKVVFCSIKE...VDWSSDKAK.ALK.TT..YF
Retrocopy FVEEKTKVA>KLANG*KKMDLIPRAKLDSSETTR<VKKKVVFCSIKEGPQVDWSSDKAKVALKFTTLGYF

Parental  LLQVLLKFRTDKGRDPSSDTFGEDSELLLQIRNDVLDSLGVNPDLLPEDFV
          LLQ.LLKF.T.KGRD.SS.TFG.DSELLLQ..N..LDSL.V.PDLLPED..
Retrocopy LLQELLKFCTSKGRDTSSVTFGGDSELLLQV*NNMLDSLVVSPDLLPEDTI

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	51.03 RPM
SRP017611_brain	0.00 RPM	64.31 RPM
SRP017611_kidney	0.00 RPM	34.01 RPM
SRP017611_liver	0.00 RPM	8.85 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1705 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1705 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1705 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004180	1 retrocopy	retro_cfam_1705 ,
Dipodomys ordii	ENSDORG00000012199	1 retrocopy	retro_dord_638,
Homo sapiens	ENSG00000142230	1 retrocopy	retro_hsap_829,
Gorilla gorilla	ENSGGOG00000013078	1 retrocopy	retro_ggor_679,
Macaca mulatta	ENSMMUG00000009506	1 retrocopy	retro_mmul_1087,
Nomascus leucogenys	ENSNLEG00000002965	1 retrocopy	retro_nleu_261,
Nomascus leucogenys	ENSNLEG00000002966	1 retrocopy	retro_nleu_262,
Pongo abelii	ENSPPYG00000010168	1 retrocopy	retro_pabe_742,
Pan troglodytes	ENSPTRG00000011202	1 retrocopy	retro_ptro_579,