RetrogeneDB ID: retro_rnor_2500

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:10226773..10227481(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Stx8
• Ensembl ID: ENSRNOG00000003849
• Aliases: None
• Description: Syntaxin-8 [Source:UniProtKB/Swiss-Prot;Acc:Q9Z2Q7]

Sequence

>retro_rnor_2500
ATGGCCCCAGACCCCTGGTTCTCCACTTACGATTCTACTTGTCAGTTTGCCCAAGAAATTGCTGAGAAGATTCAAGAACG
AAATCAGTGTGAAAGAAGAGGTGAGAAGACACCTAAGCTTACCTTGACAATCAGAACTTTGTTGAAGAATCTGAAGGTAA
AGATCGAACTCTTGAAGGACTTTACTTCTAAGAGCTATGTTGACCCGCCAGGTGACACAGCTGGAGGGGGATCGAAGAAA
GAACCTTCAGGATGACCTTGTCACCTGAGAGAGACTGCTCCTGGCATCATTTAAGAATGAGGGTTCCGAGCCGGATTTGA
TAGGTCCAGCCTGATGGGTGAAGAAGCAAAGCGAGGATCTTCCAACCCTTGGCTCTGTGAGGAGCCAGAGGAGACCAGAG
GCTTGGGTTTTGATGAGGTCCGGCAACAGCAGCAGAAAATCATAAAAGAACAGGACGCGGGTCTTGATGCCCTTTCCTCT
ACCATAAGCCGCCAAAAGCAAATGTGCCAGGAGATTGGGAATGAACTGGACGAACAGAACGAGATCATCGATGACCTTGC
CAACCTGGTGGAGAACACAGATGAGAAGCTCCGCACTGAAGCCAGGCGAGTGACCCTGGTGGACGGAAAGTCAGCTTCCT
GTGGGATGATAATGGTGATTTTATTGCTGCTCGTGGCTATTGTGGTCGTTGCAGTGTGGCCAACCAAC

Alignment

ORF - retro_rnor_2500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPDPWFSTYDSTCQIAQEIAEKIQERNQCERRGEKTPKLTLTIRTLLKNLKVKIDLLKD-LLLRAVSTR
          MAPDPWFSTYDSTCQ.AQEIAEKIQERNQCERRGEKTPKLTLTIRTLLKNLKVKI.LLKD.LLLRA..TR
Retrocopy MAPDPWFSTYDSTCQFAQEIAEKIQERNQCERRGEKTPKLTLTIRTLLKNLKVKIELLKD>LLLRAMLTR

Parental  QITQLEGDRRQNLLDDLVTRERLLLASFKNEGSEPDLI-RSSLMSEEAKRGTPNPWLCEEPEETRGLGFD
          Q.TQLEGDRR.NL.DDLVT.ERLLLASFKNEGSEPDLI.RSSLM.EEAKRG..NPWLCEEPEETRGLGFD
Retrocopy QVTQLEGDRRKNLQDDLVT*ERLLLASFKNEGSEPDLI<RSSLMGEEAKRGSSNPWLCEEPEETRGLGFD

Parental  EIRQQQQKIIQEQDAGLDALSSIISRQKQMGQEIGNELDEQNEIIDDLANLVENTDEKLRTEARRVTLVD
          E.RQQQQKII.EQDAGLDALSS.ISRQKQM.QEIGNELDEQNEIIDDLANLVENTDEKLRTEARRVTLVD
Retrocopy EVRQQQQKIIKEQDAGLDALSSTISRQKQMCQEIGNELDEQNEIIDDLANLVENTDEKLRTEARRVTLVD

Parental  RKSASCGMIMVILLLLVAIVVVAVWPTN
          .KSASCGMIMVILLLLVAIVVVAVWPTN
Retrocopy GKSASCGMIMVILLLLVAIVVVAVWPTN

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
SRP017611_brain	0.00 RPM	16.25 RPM
SRP017611_kidney	0.00 RPM	10.68 RPM
SRP017611_liver	0.00 RPM	6.32 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2500 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2500 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,