RetrogeneDB ID: retro_ocun_169

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:109907235..109908510(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000003051
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CCNA2
• Ensembl ID: ENSOCUG00000028042
• Aliases: None
• Description: cyclin A2 (CCNA2), mRNA [Source:RefSeq mRNA;Acc:NM_001257364]

Sequence

>retro_ocun_169
ATGTTGGGCCACAACGTGCCGAAGCCCGCGGCCCGCGAGGCGGGCTCGGCGCTCCTAGAGGACCAGGAGAACATCAACCC
CGAGAAGGCGGTGCACGCCCAGCAGCCGCGGGCCCAGGCTGCTCTGGCAGTACTGAAGGCTGGGAACTCCCGGGGTCCAG
TTCCACAACAGAGGCCCAAGACGCGACGGGTTGCACCTCTTAAGGATCTTCCTATAAATGATGAGCAGGTCTCTGTTCCT
CCTTGGAAAGCAAACAGTAAACAGCCTGCATTCACCATTCATGTGGATGAAGCAGAAGAGGAGCCTCCCAAGAGGCCCAC
GGAATCTAAAAAAGACAAGCCTGAAGATGTCCTGGCTTTTAATTCAGCCATCACTTTACCTGGACAAAGAAAACCACTGG
TACCTCTTGATTATCCAATGGATGGTAGTTTCGAGTCACCATATACTATGGACATGTCAATTGTATTAGAAGATGAAAAG
CCAGTGAGTGTTAATGAAGTCCCAGACTACCATGAGGATATTCACACATATCTTAGGGAAATGGAGGTTAAATGTAAACC
TAAAGTGGGTTACATGAAGAAACAGCCTGACATCACTAACAGTATGAGGGCTATCCTCGTGGACTGGTTAGTTGAAGTAG
GAGAGGAATATAAACTACAGAATGAGACTCTGCATTTGGCGGTGAACTACATCGATAGGTTTCTTTCTTCAATGTCTGTG
TTGAGAGGAAAGCTTCAGCTTGTGGGCACTGCTGCTATGCTGCTAGCCTCAAAATTTGAAGAAATATACCCACCAGAAGT
AGCAGAGTTTGTATACATTACAGATGATACCTATACAAAGAAACAAGTTCTGAGAATGGAGCATCTAGTTTTGAAAGTCC
TTGCTTTTGACTTAGCTGCACCAACGGTAAATCAGTTTCTTACCCAATACTTTCTACATCAGCAGCCTGCAAACTGCAAA
GTCGAAAGTTTAGCAATGTTTTTGGGAGAATTAAGTTTGATAGATGCTGACCCATACCTAAAGTATCTGCCATCAGTTAT
TGCTGGAGCAGCATTTCATTTAGCACTCTACACAGTCACGGGACAAAGCTGGCCTGAATCATTAGTACGAAAGACTGGAT
ACACTCTGGAGACTCTTAAGCCTTGTCTCATGGACCTTCACCAGACCTACCTCAAAGCACCACAGCATGCACAACAATCA
ATAAGAGAAAAGTACAAAAATTCAAAGTATCATGGTGTTTCCCTCCTCAACCCACCAGAGACACTAAATGTCTAA

Alignment

ORF - retro_ocun_169 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLGHNVPKPAAREAGSALLEDQENINPEKAVHAQQPRAQAALAVLKAGNSRGPVPQQRPKTRRVAPLKDL
          MLGHNVPKPAAREAGSALLEDQENINPEKAVHAQQPRAQAALAVLKAGNSRGPVPQQRPKTRRVAPLKDL
Retrocopy MLGHNVPKPAAREAGSALLEDQENINPEKAVHAQQPRAQAALAVLKAGNSRGPVPQQRPKTRRVAPLKDL

Parental  PINDEQVSVPPWKANSKQPAFTIHVDEAEEEPPKRPTESKKDKPEDVLAFNSAITLPGQRKPLVPLDYPM
          PINDEQVSVPPWKANSKQPAFTIHVDEAEEEPPKRPTESKKDKPEDVLAFNSAITLPGQRKPLVPLDYPM
Retrocopy PINDEQVSVPPWKANSKQPAFTIHVDEAEEEPPKRPTESKKDKPEDVLAFNSAITLPGQRKPLVPLDYPM

Parental  DGSFESPHTMDMSIVLEDEKPVSVNEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWL
          DGSFESP.TMDMSIVLEDEKPVSVNEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWL
Retrocopy DGSFESPYTMDMSIVLEDEKPVSVNEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWL

Parental  VEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTK
          VEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTK
Retrocopy VEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTK

Parental  KQVLRMEHLVLKVLAFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGA
          KQVLRMEHLVLKVLAFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGA
Retrocopy KQVLRMEHLVLKVLAFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGA

Parental  AFHLALYTVTGQSWPESLVRKTGYTLETLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPE
          AFHLALYTVTGQSWPESLVRKTGYTLETLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPE
Retrocopy AFHLALYTVTGQSWPESLVRKTGYTLETLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPE

Parental  TLNV
          TLNV
Retrocopy TLNV

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	5.30 RPM
SRP017611_kidney	0.00 RPM	2.23 RPM
SRP017611_liver	0.00 RPM	2.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_169 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_169 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004943	1 retrocopy	retro_btau_1335,
Macropus eugenii	ENSMEUG00000000128	1 retrocopy	retro_meug_32,
Myotis lucifugus	ENSMLUG00000005161	1 retrocopy	retro_mluc_400,
Monodelphis domestica	ENSMODG00000018931	1 retrocopy	retro_mdom_1309,
Oryctolagus cuniculus	ENSOCUG00000009143	1 retrocopy	retro_ocun_676,
Oryctolagus cuniculus	ENSOCUG00000015589	1 retrocopy	retro_ocun_1277,
Oryctolagus cuniculus	ENSOCUG00000028042	1 retrocopy	retro_ocun_169 ,