RetrogeneDB ID: retro_cfam_1959

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:42467749..42468276(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000016495
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STX8
• Ensembl ID: ENSCAFG00000017413
• Aliases: None
• Description: syntaxin 8 [Source:HGNC Symbol;Acc:11443]

Sequence

>retro_cfam_1959
CCCTGGTTCTCCACATACGACTCTACCTGCCAAATTGCACAAGAGATTGCCGAGAAAATCCAACAGCAAAATCAGTATGA
AAGAAATGGTGAAAATACAATCAGGCTTACCGTGACAATCAGAACTTTGTTGCAGAATCTGAAGGAAAAGATCGCCTTTT
TGAAGGACTTATTGCTAAATGCTGTGTCAACACATCAGATCACACAGCTTGAAGGAGACCAAAGACAGAACCTCCTGGAT
GAACTCATAACTCGAGAGAGACTGCTTGTGGCATCTTTTAAGAACGAGGGTGCAGAACCGGATCTCATCAGGTCCAGCTT
GATGACTGCAGGGGCTAAGCCAGGAGTCCCCAACCCTTGGCTCTTGAGGAGCCAGAGGAGGCCAGAGGTTTGGGTTTTGA
TGAAATCCAACAACAGCAGCAGAAGATTATCCAAGAACGGGATGCAGGCCTGGATGCCCTGTCCTCTATCATAAGTCGCC
AGAAACAGATGGGGAAGGAAATTGGGAACGAACTGGATGAACAAAAC

Alignment

ORF - retro_cfam_1959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSFSTYDSTCQIAQEIAEKIQQQNQYERNGENTIRLTVTIRTLLQNLKEKIALLKDLLLNAVSTHQITQL
          P.FSTYDSTCQIAQEIAEKIQQQNQYERNGENTIRLTVTIRTLLQNLKEKIA.LKDLLLNAVSTHQITQL
Retrocopy PWFSTYDSTCQIAQEIAEKIQQQNQYERNGENTIRLTVTIRTLLQNLKEKIAFLKDLLLNAVSTHQITQL

Parental  EGDRRQNLLDELVTRERLLVASFKNEGAEPDLIRSSLMTGGAKRGVANPWL-FEEPEETRGLGFDEIRQQ
          EGD.RQNLLDEL.TRERLLVASFKNEGAEPDLIRSSLMT.GAK.GV.NPWL..EEPEE.RGLGFDEI.QQ
Retrocopy EGDQRQNLLDELITRERLLVASFKNEGAEPDLIRSSLMTAGAKPGVPNPWL<LEEPEEARGLGFDEIQQQ

Parental  QQKIIQEQDAGLDALSSIISRQKQMGKEIGNELDEQN
          QQKIIQE.DAGLDALSSIISRQKQMGKEIGNELDEQN
Retrocopy QQKIIQERDAGLDALSSIISRQKQMGKEIGNELDEQN

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	1.51 RPM	28.22 RPM
SRP017611_brain	1.59 RPM	27.15 RPM
SRP017611_kidney	1.78 RPM	42.40 RPM
SRP017611_liver	0.51 RPM	8.92 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1959 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1959 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1959 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002045	1 retrocopy	retro_amel_911,
Canis familiaris	ENSCAFG00000017413	1 retrocopy	retro_cfam_1959 ,
Cavia porcellus	ENSCPOG00000002114	1 retrocopy	retro_cpor_1034,
Felis catus	ENSFCAG00000008276	1 retrocopy	retro_fcat_634,
Myotis lucifugus	ENSMLUG00000008612	1 retrocopy	retro_mluc_2329,
Mustela putorius furo	ENSMPUG00000007815	2 retrocopies	retro_mputfur_975, retro_mputfur_996,
Pteropus vampyrus	ENSPVAG00000001001	1 retrocopy	retro_pvam_147,
Rattus norvegicus	ENSRNOG00000003849	2 retrocopies	retro_rnor_2422, retro_rnor_2500,
Tarsius syrichta	ENSTSYG00000010795	1 retrocopy	retro_tsyr_1906,