RetrogeneDB ID: retro_pabe_546

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:87079291..87081004(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHQ1
• Ensembl ID: ENSPPYG00000013717
• Aliases: None
• Description: SHQ1, H/ACA ribonucleoprotein assembly factor [Source:HGNC Symbol;Acc:25543]

Sequence

>retro_pabe_546
ATGCTGACCCCGGCGTTCGACCTCATCCAGGAGCCAGACTTCCTGACCATCGCCATCCGCGTGCCCTACGCCCGGGCCTC
CGAGTTCGACGTCTACTTCGAGGGGTCGGACTAGACTACTATGCCAAGCCGTACTTTCTCAGATTAACCCCTCCTGGAAG
AATTGTACAAAATGGAAGCGAGCAAGGGTTCTATGATGCAGATAAAGGAATTTTTACCATTTGCCTGCCCAAAGAAACCC
CTGGCCAGCATTTTGAGGGGCTGAACATGTGTTGCTCTTCTGGCACCAGGAAAATCCGGGACAGCAAAACCACTTGTGGA
AGAAATAGGTGATTCTGAAATTCCTGAGGAAGTAGCTGACAATGAAGAGTTTGATTGGGAAATTGAGCAGACACCCTATA
AAGGGGTAACAGAAAGTGCTTTGAATCCTCAATGCCACTATGGGTTTGGAAACTTACGATCAGGAGTGTTTCAGCAGTTA
CAGGGTGAATTGAGTGATGTTATTAAGGATCCAGATTTCACCCCCGCAGCAGAAGGAAAACAAAAGCACCTGGCCGCTTA
GCTGGCCAAGTTTGATCCTGATCATTATCTAGCTGACTTTTTTGAAGATGAGGCAGTTGAACAGATTTTGAAGTATAATC
CCTGGTGGACTGACAAATATTAAAAACCGACAGCCTTTTTGGAAAAGAGTCAGAAGCAAGAAAATCATGCTGCATTAGTG
TCTTTTTCTGAAGAAGAGAAATATCAGCTACAAGAATCTGTCAATAAATCTTATCTGCTAGACAACAGAGCCTGTCGTCA
AGTGTACTACAGTTTGATTGATATCCTTTTGGCATATTGCTAAGAAACCCATGTCACTGAAGGAGAGAAGAACGTTGAAT
CTGCATGGAATATTAGGAAACTGAGTCCAATACTATCCTGGTTTGAGACTTGGACTAATGTTCATGATATCATGGTGTCT
TGGAAGAAGGGTATTGTGTTACCCACTCTATCGCCATTTCAAACTGGCGATGAAGGCCTACGGGGAGACTATAAAGATAC
TGCAACTAGGTAAAAGTGCAGTTTTAAAGTGTCTCCTGGATATTCACAAAATTTTTCAGGAAAACGACCCAGCATACATA
CTGAATGATCTCTACATCTCAGACTACTGTGTGTGGATTCAGAAAGTCAAATCCAAAACATTGGCAGCTGTTGCAAAAGC
CTTAAAGGAAGTCTCCCTTACAAAGGCCCAGTTGGGGTTAGAACTGGAAGAACTAGAAGCAGCAGCACTTCTTGTCCAGG
AGGAAGAATCTGCATTACAAGCAGCCCATTCAGTTTCTGGGCAGCAGAAACTTTGCTGTGGCTCTGAGGCAAGTGATTCG
GAGGACTCAGACAGCACTGTGTCATCTGGAAACGAGTACTCAGACTCACATTCAGAACAAGATGAACTTAAAGATAGTCC
GTGTGAGACAGTTCTTTGCAAGGTCCCCTTCTTGAAGAAAGCAGTGCCCTTCTTATTGCTGATGGTGGAGTATGCAGAAA
CACAGCCATCCAGGAGTCTGATGCCAGTCAGGGAAAGCCACTTGCCTCTTCCCGGCCTCTTGGAGTGTCTGGGCCTCTGA
TAGAGGAGCTTGGGGAACAACTGAAGACCACAGTTCAGGTTTTTGAACCCAAGGGCACCACTGCTGTAGACCATAGCAAT
ATGCAGGAGAGAGATGGCTGTCAGACACCAAAT

Alignment

ORF - retro_pabe_546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.41 %
• Parental protein coverage: 99.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLTPAFDLSQDPDFLTIAIRVPYARVSEFDVYFEGSD-FKFYAKPYFLRLTLPGRIVENGSEQGSYDADK
          MLTPAFDL.Q.PDFLTIAIRVPYAR.SEFDVYFEGSD....YAKPYFLRLT.PGRIV.NGSEQG.YDADK
Retrocopy MLTPAFDLIQEPDFLTIAIRVPYARASEFDVYFEGSD<LDYYAKPYFLRLTPPGRIVQNGSEQGFYDADK

Parental  GIFTIRL-PKETPGQHFEGLNMLTALLAPRKSRTAKPLVEEIGASEIPEEVVDDGEFDWEIEQTPYEEVS
          GIFTI.L.PK........G.....ALLAP.KS.TAKPLVEEIG.SEIPEEV.D..EFDWEIEQTPY..V.
Retrocopy GIFTICL>PKKPLASILRG*TCV-ALLAPGKSGTAKPLVEEIGDSEIPEEVADNEEFDWEIEQTPYKGVT

Parental  ESDLNPQCHYGFGNLRSGVLQRLQDELSDVIDVKDPDFTSAAERRQKRLAAELAKFDPDHYLADFFEDEA
          ES.LNPQCHYGFGNLRSGV.Q.LQ.ELSDVI..KDPDFT.AAE..QK.LAA.LAKFDPDHYLADFFEDEA
Retrocopy ESALNPQCHYGFGNLRSGVFQQLQGELSDVI--KDPDFTPAAEGKQKHLAA*LAKFDPDHYLADFFEDEA

Parental  IEQILKYNPWWTDKYSKMTAFLEKSQEQENHATLVSFSEEEKYQLRKFVNKSYLLDKRACRQVYYSLIDI
          .EQILKYNPWWTDKY.K.TAFLEKSQ.QENHA.LVSFSEEEKYQL...VNKSYLLD.RACRQVYYSLIDI
Retrocopy VEQILKYNPWWTDKY*KPTAFLEKSQKQENHAALVSFSEEEKYQLQESVNKSYLLDNRACRQVYYSLIDI

Parental  LLAYCYETRVTEGEKNVESAWNIRKLSPTLCWFETWTNVHDIMVSFGRRVLCYPLYRHFK-LVMKAYRDT
          LLAYC.ET.VTEGEKNVESAWNIRKLSP.L.WFETWTNVHDIMVS........P....F..L.MKAY..T
Retrocopy LLAYC*ETHVTEGEKNVESAWNIRKLSPILSWFETWTNVHDIMVSW-KKGIVLPTLSPFQ>LAMKAYGET

Parental  IKILQLGKSAVLKCLLDIHKIFQENDPAYILNDLYISDYCVWIQKVKSKKLAALAEALKEVSLTKAQLGL
          IKILQLGKSAVLKCLLDIHKIFQENDPAYILNDLYISDYCVWIQKVKSK.LAA.A.ALKEVSLTKAQLGL
Retrocopy IKILQLGKSAVLKCLLDIHKIFQENDPAYILNDLYISDYCVWIQKVKSKTLAAVAKALKEVSLTKAQLGL

Parental  ELEELEAAALLVQEEETALKAAHSVSGQQTLCSSSEASDSEDLDSTVSSGNEDSDSDSEQDELQDSPSET
          ELEELEAAALLVQEEE.AL.AAHSVSGQQ.LC..SEASDSED.DSTVSSGNE.SDS.SEQDEL.DSP.ET
Retrocopy ELEELEAAALLVQEEESALQAAHSVSGQQKLCCGSEASDSEDSDSTVSSGNEYSDSHSEQDELKDSPCET

Parental  VNSLQGPF-LEESSALLIVDGGVRRNTAIQESDASQGKSLASSQPLGVSGPLIEELGEQLKTTVQVSEPK
          V.....PF.LEESSALLI.DGGV.RNTAIQESDASQGK.LASS.PLGVSGPLIEELGEQLKTTVQV.EPK
Retrocopy V-LCKVPF<LEESSALLIADGGVCRNTAIQESDASQGKPLASSRPLGVSGPLIEELGEQLKTTVQVFEPK

Parental  GTTAVNRSNTQERDGCQTPN
          GTTAV..SN.QERDGCQTPN
Retrocopy GTTAVDHSNMQERDGCQTPN

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	0.11 RPM	2.82 RPM
SRP007412_cerebellum	0.00 RPM	4.13 RPM
SRP007412_heart	0.09 RPM	2.74 RPM
SRP007412_kidney	0.07 RPM	3.08 RPM
SRP007412_liver	0.03 RPM	3.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_546 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_546 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015131	1 retrocopy	retro_cjac_1045,
Homo sapiens	ENSG00000144736	1 retrocopy	retro_hsap_674,
Gorilla gorilla	ENSGGOG00000034818	1 retrocopy	retro_ggor_581,
Nomascus leucogenys	ENSNLEG00000002731	1 retrocopy	retro_nleu_463,
Pongo abelii	ENSPPYG00000013717	1 retrocopy	retro_pabe_546 ,
Pan troglodytes	ENSPTRG00000015106	1 retrocopy	retro_ptro_486,