RetrogeneDB ID: retro_pabe_2494

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:176508754..176509464(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLNS1A
• Ensembl ID: ENSPPYG00000003712
• Aliases: CLNS1A, ICLN
• Description: methylosome subunit pICln [Source:RefSeq peptide;Acc:NP_001126440]

Sequence

>retro_pabe_2494
ATGAGCTTCTTCAAAAGTTTCCCACTGTCTGGGCCAGTGGAGGGGCTCCTGCAGCAGCAGCCAGACACCAAGGCTGTGGT
AAATGGGAAGGGCCTCGGCACCAGTACCCTTTACATCACTGAGAGCCACCTGTCTTGGTTAGATGGCTCTGGATTAAGAT
TCTCACTGGAATACCCCACCATTTGTTTACATGCATTGTCCAGGGACTGAAGCGGCTATCTAGGAGAGCATTTGTATGTT
ATGGTGAAAGCTAAATTTGAAGATGGATAAAAAGAATCTGTTGCTGATGAAGAAGAGGAAAATAGTGATAATGATGTAGA
ACCTATTACTGAATTTAGATTTGTGCCTAGTGATAAATCAGCATTGGAGGCAATGTTCACTGCAATGTGTGAATGTCAGT
ACTTGCATCCAGATGCTGAGGATGAAGATTCAGATGCTTATGATGGAGAAGAATATGATCTGGAAGTGCAAGAACAAGGA
CATGGGGAGATCCCTACATTTTACACCTATGGAGAAGGATTTATCTCATCTAACAGCAGAGGGCCAAGCCATGTTGGAGA
TTAGAAGGAACGCTTTCTCAGTCTGTAAGCTGCCAGTATCATATGGCTGGGGTCAGGACAGAAGACTCAATAAGAGATGA
TGAAGCTGGGATGGAGGCAGATACCACACCAACAGTTGCTGGATAGTTTGAGGATGCAGATGTTGATCAC

Alignment

ORF - retro_pabe_2494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSFLKSFPPPGPAEGLLRQQPDTEAVLNGKGLGTGTLYIAESRLSWLDGSGLGFSLEYPTISLHALSRDR
          MSF.KSFP..GP.EGLL.QQPDT.AV.NGKGLGT.TLYI.ES.LSWLDGSGL.FSLEYPTI.LHALSRD.
Retrocopy MSFFKSFPLSGPVEGLLQQQPDTKAVVNGKGLGTSTLYITESHLSWLDGSGLRFSLEYPTICLHALSRD*

Parental  SDCLGEHLYVMVNAKFEEESKEPVADEEEEDSDDDVEPITEFRFVPSDKSALEAMFTAMCECQALHPDPE
          S..LGEHLYVMV.AKFE...KE.VADEEEE.SD.DVEPITEFRFVPSDKSALEAMFTAMCECQ.LHPD.E
Retrocopy SGYLGEHLYVMVKAKFEDG*KESVADEEEENSDNDVEPITEFRFVPSDKSALEAMFTAMCECQYLHPDAE

Parental  DEDSDDYDGEEYDVEAHEQGQGDIPTFYTYEEGLSHLTAEGQATLE-RLEGMLSQSVSSQYNMAGVRTED
          DEDSD.YDGEEYD.E..EQG.G.IPTFYTY.EG.......G......RLEG.LSQSVS.QY.MAGVRTED
Retrocopy DEDSDAYDGEEYDLEVQEQGHGEIPTFYTYGEGFISSNSRGPSHVG<RLEGTLSQSVSCQYHMAGVRTED

Parental  SIRDYEDGMEVDTTPTVAGQFEDADVDH
          SIRD.E.GME.DTTPTVAG.FEDADVDH
Retrocopy SIRDDEAGMEADTTPTVAG*FEDADVDH

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	35.39 RPM
SRP007412_cerebellum	0.00 RPM	42.20 RPM
SRP007412_heart	0.00 RPM	24.05 RPM
SRP007412_kidney	0.00 RPM	23.97 RPM
SRP007412_liver	0.00 RPM	24.51 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2494 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2494 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3010
Gorilla gorilla	retro_ggor_2084

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019930	1 retrocopy	retro_btau_376,
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Homo sapiens	ENSG00000074201	2 retrocopies	retro_hsap_3010, retro_hsap_3595,
Gorilla gorilla	ENSGGOG00000003091	1 retrocopy	retro_ggor_2084,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Mus musculus	ENSMUSG00000025439	1 retrocopy	retro_mmus_1984,
Nomascus leucogenys	ENSNLEG00000016699	2 retrocopies	retro_nleu_300, retro_nleu_756,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Pongo abelii	ENSPPYG00000003712	1 retrocopy	retro_pabe_2494 ,
Sorex araneus	ENSSARG00000009460	2 retrocopies	retro_sara_247, retro_sara_682,
Ictidomys tridecemlineatus	ENSSTOG00000027980	3 retrocopies	retro_itri_239, retro_itri_319, retro_itri_490,