RetrogeneDB ID: retro_ocun_1551

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018699:8490156..8491603(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPRA
• Ensembl ID: ENSOCUG00000021376
• Aliases: None
• Description: protein tyrosine phosphatase, receptor type, A [Source:HGNC Symbol;Acc:9664]

Sequence

>retro_ocun_1551
TACATCAACTCTTCATTCATCAATGGCTACCAAGAAAAGAAAAAATTCATAACTGCACAAGGACGAAAAGAAGAAATGGT
GAATGATTTCTGGAGGATGATCTGGGAACAAAACACAGCTACCATTGTCATGGTGACCAACCTAAAGGAGAGAAAGGAGT
GTAAGTGTGCCCAGTATTGGCCAGACCAAGGCTGCTAGACCTATGGGAATATCCACGTGTCTGTTAAGGATGTGACTGTC
CTAGTGGACTACATAGTATGGAAGTTCTGCATCCAGCAGGTGGGTGACATAACCAACAGAAAGCCCCAGCGCCTCATCAC
TCAGTTCCACTTCACCAGCTGGCAGGACTTCGGGGTACCTTTCAACCCGATTGGCATGCTCAAGTTCCTCAAGAAGTTGA
AAGCCTGTAACCCTCAGTATGCAGGGGCCGTCATGGCCTATTGCAGCGCTGGTGAAGGGCGTGCAGGTACCTTTCTCATC
ATTGATGCCATGCTGGACATGACGCACACAGAGCGGAAGGTGGACGTGTACAGCTTTGTGAGCCGGATCCGGGCACAGCA
TTGCCAGATGGTGCAAACAGATATGCAGTATGCCTTCATATACCAGCCCTTCTGGAGCATTATCTGTATGGGGATACAGA
ACTGGAAGTGACCTCTCTAGAAACCCACTTACAGAAGATTTACAACAAAATCTCAGGGACCAGCAACAATGGGTTAGAGG
AGGAGTTCAAGAAGTTAACATCAATCAAAATCCAGAATGACAAGATGCGGACTGGGAACCTCCCAGCCAACATGAAGAAG
AACCGAGTTTTACAGATCATTCCGTATGAATTCAACAGAGTGATCATTCCAGTCAAGTGGGGCGAGGAGAACACAGACTA
CGTGAATGCATCCCTCATCGATGGCTACCGGCAGAAGGACTCCTACGTTGCCAGCCAGGGCCCTCTTCTCCACACCATTG
AGGACTTCTGGCGAATGATCTGGGAGTGGAAATCCTGCTCTATCGTGATGCTGACAGAACTGGAAGAGAGAGGCCAGGAG
AAGTGTGCCCAGTACTGGCCTCCTGATGGGCTAGTGTCCTATGGAGACATCACAGTGAAGCTGAGGAAGAAAGAGGAATG
TGAGAGCTACACCATCCGAGACCTCCTGGTCACCAACACCAGGGAGAACAAGAGCCGGCAGATCCGGCAGTTCCACTTCC
ATGCTGGCCTGAAGTGGGGATTCCCAGCGATGGGAAGGGCATGATCAGCATCATTGTGGCCGTGCAGAAGCAGCAACAGC
CGTCAGGGAGCCACCCCATCACCGTGCACTGCAGCGCTGGGGCAGGACAGACAGGGACCTTCTGTGCCCTGAGCACAGTC
CTGGAGTGCGTGAAAGCAGAGGGGATCCCGGATATTTTCCAGACTGTCAAGAACCTAAGGCTGCAGCGGCCACACATGGT
CCAGACA

Alignment

ORF - retro_ocun_1551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.52 %
• Parental protein coverage: 59.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YINASFINGYQEKNKFIAAQGPKEETVNDFWRMIWEQNTATIVMVTNLKERKECKCAQYWPDQGCWTYGN
          YIN.SFINGYQEK.KFI.AQG.KEE.VNDFWRMIWEQNTATIVMVTNLKERKECKCAQYWPDQGC.TYGN
Retrocopy YINSSFINGYQEKKKFITAQGRKEEMVNDFWRMIWEQNTATIVMVTNLKERKECKCAQYWPDQGC*TYGN

Parental  IRVSVEDVTVLVDYTVRKFCIQQVGDVTNRKPQRLITQFHFTSWPDFGVPFTPIGMLKFLKKVKACNPQY
          I.VSV.DVTVLVDY.V.KFCIQQVGD.TNRKPQRLITQFHFTSW.DFGVPF.PIGMLKFLKK.KACNPQY
Retrocopy IHVSVKDVTVLVDYIVWKFCIQQVGDITNRKPQRLITQFHFTSWQDFGVPFNPIGMLKFLKKLKACNPQY

Parental  AGAIVVHCSAGVGRTGTFVVIDAMLDMMHTERKVDVYGFVSRIRAQRCQMVQTDMQYVFIYQ-ALLEHYL
          AGA....CSAG.GR.GTF..IDAMLDM.HTERKVDVY.FVSRIRAQ.CQMVQTDMQY.FIYQ.ALLEHYL
Retrocopy AGAVMAYCSAGEGRAGTFLIIDAMLDMTHTERKVDVYSFVSRIRAQHCQMVQTDMQYAFIYQ<ALLEHYL

Parental  YGDTELEVTSLETHLQKIYNKIPGTSNNGLEEEFKKLTSIKIQNDKMRTGNLPANMKKNRVLQIIPYEFN
          YGDTELEVTSLETHLQKIYNKI.GTSNNGLEEEFKKLTSIKIQNDKMRTGNLPANMKKNRVLQIIPYEFN
Retrocopy YGDTELEVTSLETHLQKIYNKISGTSNNGLEEEFKKLTSIKIQNDKMRTGNLPANMKKNRVLQIIPYEFN

Parental  RVIIPVKRGEENTDYVNASFIDGYRQKDSYIASQGPLLHTIEDFWRMIWEWKSCSIVMLTELEERGQEKC
          RVIIPVK.GEENTDYVNAS.IDGYRQKDSY.ASQGPLLHTIEDFWRMIWEWKSCSIVMLTELEERGQEKC
Retrocopy RVIIPVKWGEENTDYVNASLIDGYRQKDSYVASQGPLLHTIEDFWRMIWEWKSCSIVMLTELEERGQEKC

Parental  AQYWPSDGLVSYGDITVELKKEEECESYTVRDLLVTNTRENKSRQIRQFHFHG-WPEVGIPSDGKGMISI
          AQYWP.DGLVSYGDITV.L.K.EECESYT.RDLLVTNTRENKSRQIRQFHFH..WPEVGIPSDGKGMISI
Retrocopy AQYWPPDGLVSYGDITVKLRKKEECESYTIRDLLVTNTRENKSRQIRQFHFHA<WPEVGIPSDGKGMISI

Parental  IAAVQKQQQQSGNHPITVHCSAGAGRTGTFCALSTVLERVKAEGILDVFQTVKSLRLQRPHMVQT
          I.AVQKQQQ.SG.HPITVHCSAGAG.TGTFCALSTVLE.VKAEGI.D.FQTVK.LRLQRPHMVQT
Retrocopy IVAVQKQQQPSGSHPITVHCSAGAGQTGTFCALSTVLECVKAEGIPDIFQTVKNLRLQRPHMVQT

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	0.06 RPM	224.84 RPM
SRP017611_kidney	0.00 RPM	87.27 RPM
SRP017611_liver	0.08 RPM	38.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1551 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1551 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000021376	1 retrocopy	retro_ocun_1551 ,