RetrogeneDB ID: retro_ocun_1043

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:65738574..65739186(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPN1
• Ensembl ID: ENSOCUG00000013637
• Aliases: None
• Description: GPN-loop GTPase 1 [Source:HGNC Symbol;Acc:17030]

Sequence

>retro_ocun_1043
TCCAATGTGCTCTGTACCTGCAGCATCTTATACAGAACTAAGCTGCCTTTCATTGTGGTTGGGAATAAAACTGACATCAC
TGACCACATTTTGCAGTGGATTGGATGCAGGATTCTAAGGATTTTTAAGATGCTTTGAATCAAGAAACTACATATATCAG
TATAACTTGTTCAATGAACCTGGTGCTGGATGAGTTTCACAGCTCACTCCAGGTGGTAGGTGTCTCTTCTAATCTGAGTT
CTGGCTTAGATGAACTCTTGGTGCATATCATCAGTGTTGCAGAAGAATATGAAAGGGAGTAAGGTCCTGAACATGAGCTT
CTGAAGAAATCACTGGCCAGTGAACAAAGCCAGCAGCAAAAAGAACAGTTGAAATGCTTTCAGAAAGATATGGGCTCTGT
AGCCTTGGACACAGAAACTGCCAAAGACAGTCTGTCTCATGTGCTGGGCCCTTCTGCAGTGATTCTGACTTGAGGAACTT
GAATGAAGAGGATGAGAAACTGACAGTGATGTTGATGACACTGACCCAGAGTTACAGAAGAAGTCATGAAGTGCCAGCAT
TCCAGAGGGTATGCAAAAATCACTGGCACAGTACAAACAGAGAAAAAACAAA

Alignment

ORF - retro_ocun_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.44 %
• Parental protein coverage: 55.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NNVWCLVFSILYKTKLPFIVVMNKTDIIDH-SFAVEWMQDFEAFQDALNQETTYVSNLTRSMSLVLDEFY
          .NV.C...SILY.TKLPFIVV.NKTDI.DH..FAV.WMQD...F.DALNQETTY.S..T.SM.LVLDEF.
Retrocopy SNVLCTC-SILYRTKLPFIVVGNKTDITDH<HFAVDWMQDSKDF*DALNQETTYIS-ITCSMNLVLDEFH

Parental  SSLRVVGVSSVLGTGLDELFVHVTSAAEEYEREYRPEYERLKKSLIQASAQSQQQKEQLERLRKDMGSVA
          SSL.VVGVSS.L..GLDEL.VH..S.AEEYERE..PE.E.LKKSL..AS.QSQQQKEQL....KDMGSVA
Retrocopy SSLQVVGVSSNLSSGLDELLVHIISVAEEYERE*GPEHELLKKSL--ASEQSQQQKEQLKCFQKDMGSVA

Parental  LDTGAAKDSLSPVLEPSDLILTRGT-LDEEDE-EADSDTDDID-HRVTEE-SHEEPAFQNF-MQESMAQY
          LDT..AKDSLS.VL.PS..ILT.GT.L.EEDE.E.DSD.DD.D..RVTEE.SHE.PAFQ...MQ.S.AQY
Retrocopy LDTETAKDSLSHVLGPSAVILT*GT<LNEEDE<ETDSDVDDTD<PRVTEE<SHEVPAFQRV<MQKSLAQY

Parental  WKRNDK
          ..R..K
Retrocopy KQRKNK

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	13.30 RPM
SRP017611_kidney	0.00 RPM	13.28 RPM
SRP017611_liver	0.00 RPM	8.56 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1043 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1043 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	ENSOCUG00000013637	1 retrocopy	retro_ocun_1043 ,