RetrogeneDB ID: retro_ocun_408

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:161185135..161185981(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCPEP1
• Ensembl ID: ENSOCUG00000011355
• Aliases: None
• Description: serine carboxypeptidase 1 [Source:HGNC Symbol;Acc:29507]

Sequence

>retro_ocun_408
AAAATGGCTGCTGGTATTGGTCTAGAACTTCATAAGGCTGTGCAGCAAGGGACCATCAAGTGCAATTTCTCTGGGGTTGC
CTTGGGTGACTCCTGGATCTCCCCTGTTGATTCGGTGCTCTCCTGGGGACCTTACCTGTACAGCATGTCTCTCCTGGACG
ACCAAGGTCTGGCGGAGGTATCTCATGTTGCTGAGCAAGTCCTGGATGCCGTCAACAAGGGGCTCTACAAGGAAGCCACT
CAGCTGTGGGAGAAAGCAGAAATGGTCATTGAGAAGAACACGGACGGGGTGAACTTCTACAACATCTTAACCAAAGACAC
TCCCATGTCTTCCATGGAATCCAGCCTGGAATTCATGCGGAGCCACTTGGTTCGTCTGTGTCAGCGTCACGTGAGACACC
TACATGGAGATTCCTTGAGTCAGCTCATGAATGGTCCCATCAGAAAGAAACTCAAAATTATTCCTGAAGATTTCTCCTGG
GGAGCCCAATCTTCCAATGTCTTCATGAACATGGAGGGGGACTTCATGAAGCCGGTCATCAGCATTGTGGATGAGCTGCT
GGAAGCCGGGGTCAATGTGACCGTGTATAATGGCCAGCTCGACCTCATCGTGGACACCATGGGTCAGGAGGCCTGGGTGC
GGAAGCTGAAGTGGCCAGAACTGCCCAAATTCAATCAGCTGAGGTGGAAGGCCCTGTACAGCGACCCCAAATCCTCTGAA
ACATCTGCTTTTGTCAAGTCCTACAAGAACCTGGCTTTCTACTGGATTCTAAGAGCTAGCCACATGGTTCCCTCTGACCA
AGGGGACATGGCTCTGAAGATGATGAAGTTGGTGACTCAGCAAGAA

Alignment

ORF - retro_ocun_408 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.29 %
• Parental protein coverage: 61.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMAAGIGLELYKAVQQGTIKCNFSGVALGDSWISPVDSVLSWGPYLYSMSLLDDQGLAEVSHVAEQVLDA
          KMAAGIGLEL.KAVQQGTIKCNFSGVALGDSWISPVDSVLSWGPYLYSMSLLDDQGLAEVSHVAEQVLDA
Retrocopy KMAAGIGLELHKAVQQGTIKCNFSGVALGDSWISPVDSVLSWGPYLYSMSLLDDQGLAEVSHVAEQVLDA

Parental  VNKGLYKEATQLWEKAEMVIEKNTDGVNFYNILTKDTPMSSMESSLEFMRSHLVRLCQRHVRHLHGDSLS
          VNKGLYKEATQLWEKAEMVIEKNTDGVNFYNILTKDTPMSSMESSLEFMRSHLVRLCQRHVRHLHGDSLS
Retrocopy VNKGLYKEATQLWEKAEMVIEKNTDGVNFYNILTKDTPMSSMESSLEFMRSHLVRLCQRHVRHLHGDSLS

Parental  QLMNGPIRKKLKIIPEDFSWGAQSSNVFMNMEGDFMKPVISIVDELLEAGVNVTVYNGQLDLIVDTMGQE
          QLMNGPIRKKLKIIPEDFSWGAQSSNVFMNMEGDFMKPVISIVDELLEAGVNVTVYNGQLDLIVDTMGQE
Retrocopy QLMNGPIRKKLKIIPEDFSWGAQSSNVFMNMEGDFMKPVISIVDELLEAGVNVTVYNGQLDLIVDTMGQE

Parental  AWVRKLKWPELPKFNQLRWKALYSDPKSSETSAFVKSYKNLAFYWILRAGHMVPSDQGDMALKMMKLVTQ
          AWVRKLKWPELPKFNQLRWKALYSDPKSSETSAFVKSYKNLAFYWILRA.HMVPSDQGDMALKMMKLVTQ
Retrocopy AWVRKLKWPELPKFNQLRWKALYSDPKSSETSAFVKSYKNLAFYWILRASHMVPSDQGDMALKMMKLVTQ

Parental  QE
          QE
Retrocopy QE

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	1.38 RPM	22.08 RPM
SRP017611_kidney	23.72 RPM	182.54 RPM
SRP017611_liver	2.93 RPM	42.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_408 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_408 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	ENSOCUG00000011355	1 retrocopy	retro_ocun_408 ,