RetrogeneDB ID: retro_ocun_213

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:68811367..68813302(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026104
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000004189
• Aliases: None
• Description: None

Sequence

>retro_ocun_213
AGGGGAAAAAAAAATTTCACAAGAAAGAATACAAAGCCATCGCAAGAAAAAAGCAGATTTCCTAAAAACAGCGATTCTGG
TTCTTCAAAGACATTCCCAAGGAAAGTTACTAAGGAAGGTGGACCTAAAATCACATCAAAGAACTTTGAGAAGAGTGCCA
CAAAACCTGGGAAAAAGGGTGTGAAGCAGTTCAAGACTAAGCAACAAGGGGACAAAGGATCGAAGAACAAATTTCAGGCG
GCAAATAAATTCAGCAAGAAGAGAAAATTCCAGTCAGACAATAAAAGTGATGAATCAGCAGCCAAGAAACCCAAATGGGA
TGACTTCAAAAAGAAGAAGAAAGAACTGAAGCAGAGCAGGCAACTGAGTGATAAAACCAACTATGACATTGTTGTTCGGG
CAAAGCAGATTTGGGAGATCCTGAGAAGAAAAGACTGTGACAAAGACAAAAGAGTAAAGTTAATGAGTGACTTGCAGAAG
TTGATTCAAGGGAAAATTAAAACTATTGCATTTGCACATGATTCAACGCTTGTGATCCAGTGTTACATTCAGTATGGCAA
TGAAGAACAGAGAAGACAGGCATTTGAAGAATTGCAAGGTGATTTGGTTGAATTAAGTAAATCCAAATACTCCAGAAATA
TTGTTAAGAAATTTCTTATGTATGGAAGTAAACCACAGGTTGCAGAGATAATCAGAAGTTTTAAAGGCCATGTGCGCAAG
ATGCTGCGGCATGCAGAGGCGTCAGCTATTGTAGAGTATGCCTACAATGACAAAGCCATCTTGGAGCAGAGGAACATGCT
CACAGAGGAACTCTATGGAAATACGTTTCAGCTTTACAAGTCAGCAGATCATCCAACTCTGGACAAAGTGTTAGAGGTAC
AGCCAGAAAAATTAGAGCTTATTATGGATGAAATGAAACAGATTCTAACGCCAATGGCTCAAAAGGAAGCTGTGATTAAG
CACTCGTTGGTGCATAAAGTATTCTTGGACTTTTTTACCTATGCACCCCCAAAACTCAAATCAGAAGTGATTGAAGCTAT
CCGGGAAGCGGTGACCTACCTGGCACACACACACGATGGCGCCAGAGTGGCCATGCACTGTCTGTGGCATGGAACGCCCA
AGGACAGGAAAGTGATTGTGAAAACAATGAAATCTTATGTTGAGAAGGTGGCTAATGGCCAATATTCACATTTGGTTTTA
CTGGCAGCATTTGATTGCATTGACGATACTAAGCTTGTGAAACAGATAATCATATCAGAGATTATCAGTTCCTTGCCTAG
CATTGTAAATGACAAATATGGAAGAAAGGTCCTGTTATATTTACTAAGCCCCAGAGATCCTGCCCATCCAGTACGAGAAA
TCATCGAAGTTCTACAGAAAGGAGATGGAAATGCACACAGTAAGAAAGATACAGAGATCCGCCGACGTGAGCTCTTAGAG
TCCATTTCTCCAGCTTTGCTAAGCTACCTACAAGGACACGCCCAGGAGCTGGTGCTAGATAAGTCTGCGTGTGTGTTAGT
GTCCAGCATTCTTGGATCTGCCACGGGGGACGTCCAGCCCGCCATGGCTGCCATCGCCACCCTGGCAGCGGCACCCCTGC
ATCCTGGCGGCAGCGACGGAGAGCTTCATGTTGCGGAACATCCTGCAGGACATCTGGTTCTGAAGTGGTTGATAGAGCAA
GACAGAAAGATGAGAGAAAGTGGAAGAGAAGGTTGCTTTGCAAAAGCACTGGTAGAGCATGTTGGTGTTAAGAACCTGAA
GTCGTGGGCCAGCGTCAATCGAGGTGCCATAATCCTTTCCAGCCTTCTCCAGAGCTCTGACCAAGAAGTTGCAGGCAAAG
TCCGAGCTAGATTGAAAAGCCTGATTCCCACATTGGAAAAAAACAAAAATGCCAGCAAAGGAGTGGAAATTCTGCTTGAA
AGATTGACTGCATAG

Alignment

ORF - retro_ocun_213 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.98 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGKKKFTRKNRKPSQEKSRFPKNSDSGSSKTFPRKVTKEGGPKITSKNFEKSATKPGKKGVKQFKTRQQG
          .GKK.FTRKN.KPSQEKSRFPKNSDSGSSKTFPRKVTKEGGPKITSKNFEKSATKPGKKGVKQFKT.QQG
Retrocopy RGKKNFTRKNTKPSQEKSRFPKNSDSGSSKTFPRKVTKEGGPKITSKNFEKSATKPGKKGVKQFKTKQQG

Parental  DKGSKNKFQAANKFSKKRKFQSDNKSDESAAKKPKWDDFKKKKKELKQSRQLSDKTNYDIVVRAKQIWEI
          DKGSKNKFQAANKFSKKRKFQSDNKSDESAAKKPKWDDFKKKKKELKQSRQLSDKTNYDIVVRAKQIWEI
Retrocopy DKGSKNKFQAANKFSKKRKFQSDNKSDESAAKKPKWDDFKKKKKELKQSRQLSDKTNYDIVVRAKQIWEI

Parental  LRRKDCDKDKRVKLMSDLQKLIQGKIKTIAFAHDSTRVIQCYIQYGNEEQRRQAFEELQGDLVELSKAKY
          LRRKDCDKDKRVKLMSDLQKLIQGKIKTIAFAHDST.VIQCYIQYGNEEQRRQAFEELQGDLVELSK.KY
Retrocopy LRRKDCDKDKRVKLMSDLQKLIQGKIKTIAFAHDSTLVIQCYIQYGNEEQRRQAFEELQGDLVELSKSKY

Parental  SRNIVKKFLMYGSKPQVAEIIRSFKGHVRKMLRHAEASAIVEYAYNDKAILEQRNMLTEELYGNTFQLYK
          SRNIVKKFLMYGSKPQVAEIIRSFKGHVRKMLRHAEASAIVEYAYNDKAILEQRNMLTEELYGNTFQLYK
Retrocopy SRNIVKKFLMYGSKPQVAEIIRSFKGHVRKMLRHAEASAIVEYAYNDKAILEQRNMLTEELYGNTFQLYK

Parental  SADHPTLDKVLEVQPEKLELIMDEMKQILTPMAQKEAVIKHSLVHKVFLDFFTYAPPKLRSEMIEAIREA
          SADHPTLDKVLEVQPEKLELIMDEMKQILTPMAQKEAVIKHSLVHKVFLDFFTYAPPKL.SE.IEAIREA
Retrocopy SADHPTLDKVLEVQPEKLELIMDEMKQILTPMAQKEAVIKHSLVHKVFLDFFTYAPPKLKSEVIEAIREA

Parental  VIYLAHTHDGARVAMHCLWHGTPKDRKVIVKTMKSYVEKVANGQYSHLVLLAAFDCIDDTKLVKQIIISE
          V.YLAHTHDGARVAMHCLWHGTPKDRKVIVKTMKSYVEKVANGQYSHLVLLAAFDCIDDTKLVKQIIISE
Retrocopy VTYLAHTHDGARVAMHCLWHGTPKDRKVIVKTMKSYVEKVANGQYSHLVLLAAFDCIDDTKLVKQIIISE

Parental  IISSLPSIVNDKYGRKVLLYLLSPRDPAHTVREIIEVLQKGDGNAHSKKDTEIRRRELLESISPALLSYL
          IISSLPSIVNDKYGRKVLLYLLSPRDPAH.VREIIEVLQKGDGNAHSKKDTEIRRRELLESISPALLSYL
Retrocopy IISSLPSIVNDKYGRKVLLYLLSPRDPAHPVREIIEVLQKGDGNAHSKKDTEIRRRELLESISPALLSYL

Parental  QGHAQELVLDKSACVLVSSILGSATGDVQPAMAAIATLAAAPLHPGGSDGELHVAEHPAGHLVLKWLIEQ
          QGHAQELVLDKSACVLVSSILGSATGDVQPAMAAIATLAAAPLHPGGSDGELHVAEHPAGHLVLKWLIEQ
Retrocopy QGHAQELVLDKSACVLVSSILGSATGDVQPAMAAIATLAAAPLHPGGSDGELHVAEHPAGHLVLKWLIEQ

Parental  DRKMKESGREGCFAKALVEHVGVKNLKTWASVNRGAIILSSLLQSSDQEVAGKVRAGLKSLIPTLEKNKN
          DRKM.ESGREGCFAKALVEHVGVKNLK.WASVNRGAIILSSLLQSSDQEVAGKVRA.LKSLIPTLEKNKN
Retrocopy DRKMRESGREGCFAKALVEHVGVKNLKSWASVNRGAIILSSLLQSSDQEVAGKVRARLKSLIPTLEKNKN

Parental  ASKGVEILLERLTA
          ASKGVEILLERLTA
Retrocopy ASKGVEILLERLTA

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	0.17 RPM	9.55 RPM
SRP017611_kidney	0.30 RPM	10.03 RPM
SRP017611_liver	0.15 RPM	5.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_213 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_213 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_213 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
Ailuropoda melanoleuca	ENSAMEG00000012187	1 retrocopy	retro_amel_1752,
Callithrix jacchus	ENSCJAG00000010917	1 retrocopy	retro_cjac_2253,
Cavia porcellus	ENSCPOG00000008552	1 retrocopy	retro_cpor_1158,
Loxodonta africana	ENSLAFG00000017341	1 retrocopy	retro_lafr_1029,
Mus musculus	ENSMUSG00000041360	1 retrocopy	retro_mmus_3640,
Oryctolagus cuniculus	ENSOCUG00000004189	1 retrocopy	retro_ocun_213 ,
Sorex araneus	ENSSARG00000000579	1 retrocopy	retro_sara_499,