RetrogeneDB ID: retro_ptro_486

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:49028102..49029813(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHQ1
• Ensembl ID: ENSPTRG00000015106
• Aliases: None
• Description: None

Sequence

>retro_ptro_486
ATGCTGACCCCAGCGTTCAGCCTCAGCCAGGATCCGGATTTCCTGACCATCGCCATCCGCGTGCCCTAGGCCCCGGCCTC
CGAGTTCAACGTCTACTTCGAGGGGTCGGCCTAGACTACTATGCCAAGCCGTACTTTCTCAGATTAACCCCTCCTGGAAG
AATTGTAGAATATGGAAGCGAGCAAGGGTCCTATGATGCAGATAAAGGAATTTTTACCACTCACCTGCCCAAAGAAACCC
CTGGCCAGCATTTTGAGGGGCTGAACATGTGTTGCTCTTCTGGCACCAGGAAAATCCGGGACAGCAAAACCACTTGTGGA
AGCAATAGGTGATTCTGAAATTCCTGAGGAAGTAGTTCACGATGAAGAGTTTGATTGGGAAATTGAGCAGACACCCTATG
AAGAGGTAACAGAAAGTGCTTTGAATCCTCATGCTACTATGGGTTTGGAAACTTACGATCAGGAGTGTTTCAGCAGTTAC
AGGATGAATTGAGTGATGCTATTAAGGATCCAGATTTCACCCCTGCAGCAGAACGAAAACAAAAGCACCTGGCCGCTGAG
CTGGCCAAGTTTGATCCTGATCATTATCTAGCTGACTTTTTTGAAGATGAGGCAGTTGAACAGATTTTGAAGTATAATCC
TTGGTGGACTGACAAATATTAAAAAACGACGGCCTTTTTGGAAAAGAGTCAGAAGCAAGAAAATCATGCTGCATTAGTGT
CTTTTTCTGAAGAGAAATATCAGCTACAAGAATTTGTCAATAAATCTTATCTGCTAGACAACAGAGCCTGTCGTCAAGTG
TGCTACAGTTCGATTGATATCCTTCTGGCATATTGCTAAGAAACCCGTGTCACTGAAGGAGAGAAGAACGTTGAATCTGC
ATGGAATATCAGGAAACTGAGTCCAATACTATGCTGGTTTGAGACTTGGACTAATGTTCATGATATCATGGTGTCTTTTG
GAAGAAGGGTATTGTGTTACCCGCTCTATCGCCATTTCAAACTGGCGATGAAGGCCTACGGGGAGACTATAAAGATACTG
CAACTAGGTAAAAGTGCAGTTTTAAAGTGTCTCCTGGATATTCACAAAATTTTTCAGGAAAATGACCCAGCATACATACT
GAATGATCTCTACATCTCAGACTACTGTGTGTGGATTCAGAAAATCAAATCCAAAACGTTGGCAGCTCTTGCAGAAGCCT
TAAAGGAAGTCTCCCTTACAAAGGCCCAGTTGGGGTTAGAACTGGAAGAACTAGAAGCAGCAGCACTTCTTGTCCAGGAG
GAAGAATCTGCATTACAAGCAGCCCATTCAGTTTCTGGGCAGCAGAAACTTTGCTGCAGCTCTGAGGCAGGTGATTCAGA
GGACTCAGACAGCACTGTGTCATCTGGAAACGAAGACTCAGACTCGCATTCAGAACAAGATGAACTCAAAGATAGTCCAT
CTGAGACAGTTCTTTGCAAGGTCCCCTTCTTGAAGAAAGCAGTGCCCTTCTGATTGTTGATGGTGGAGTATGCAGAAACA
CAGCCATCCAGGAGTCTGATGCCAGTCAGGGAAAGCCACTTGCCTCTTCCCGGCCTCTTGGAGTGTCTGGGCCTCTGATA
GAGGAGCTTGGGGAACAACTGAAGACCACCGTTCAGGTTTTTGAACCCGAGGGCACCACTGCTGTAGACCACAGCAACAT
GCAGGAGAGAGATGGCTGTCAGACACCAAAT

Alignment

ORF - retro_ptro_486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.69 %
• Parental protein coverage: 99.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLTPAFDLSQDPDFLTIAIRVPYARVSEFDVYFEGS-DFKFYAKPYFLRLTLPGRIVENGSEQGSYDADK
          MLTPAF.LSQDPDFLTIAIRVP.A..SEF.VYFEGS.....YAKPYFLRLT.PGRIVE.GSEQGSYDADK
Retrocopy MLTPAFSLSQDPDFLTIAIRVP*APASEFNVYFEGS<GLDYYAKPYFLRLTPPGRIVEYGSEQGSYDADK

Parental  GIFTIRL-PKETPGQHFEGLNMLTALLAPRKSRTAKPLVEEIGASEIPEEVVDDEEFDWEIEQTPYEEVS
          GIFT..L.PK........G.....ALLAP.KS.TAKPLVE.IG.SEIPEEVV.DEEFDWEIEQTPYEEV.
Retrocopy GIFTTHL>PKKPLASILRG*TCV-ALLAPGKSGTAKPLVEAIGDSEIPEEVVHDEEFDWEIEQTPYEEVT

Parental  ESALNPQ-CHYGFGNLRSGVLQRLQDELSDVIDIKDPDFTPAAERRQKRLAAELAKFDPDHYLADFFEDE
          ESALNP..C.YGFGNLRSGV.Q.LQDELSD.I..KDPDFTPAAER.QK.LAAELAKFDPDHYLADFFEDE
Retrocopy ESALNPH<CYYGFGNLRSGVFQQLQDELSDAI--KDPDFTPAAERKQKHLAAELAKFDPDHYLADFFEDE

Parental  AIEQILKYNPWWTDKYSKMTAFLEKSQEQENHATLVSFSEEEKYQLRKFVNKSYLLDKRACRQVCYSLID
          A.EQILKYNPWWTDKY.K.TAFLEKSQ.QENHA.LVSFSEE.KYQL..FVNKSYLLD.RACRQVCYS.ID
Retrocopy AVEQILKYNPWWTDKY*KTTAFLEKSQKQENHAALVSFSEE-KYQLQEFVNKSYLLDNRACRQVCYSSID

Parental  ILLAYCYETRVTEGEKNVESAWNIRKLSPTLCWFETWTNVHDIMVSFGRRVLCYPLYRHFKLVMKAYRDT
          ILLAYC.ETRVTEGEKNVESAWNIRKLSP.LCWFETWTNVHDIMVSFGRRVLCYPLYRHFKL.MKAY..T
Retrocopy ILLAYC*ETRVTEGEKNVESAWNIRKLSPILCWFETWTNVHDIMVSFGRRVLCYPLYRHFKLAMKAYGET

Parental  IKILQLGKSAVLKCLLDIHKIFQENDPAYILNDLYISDYCVWIQKVKSKKLAALAEALKEVSLTKAQLGL
          IKILQLGKSAVLKCLLDIHKIFQENDPAYILNDLYISDYCVWIQK.KSK.LAALAEALKEVSLTKAQLGL
Retrocopy IKILQLGKSAVLKCLLDIHKIFQENDPAYILNDLYISDYCVWIQKIKSKTLAALAEALKEVSLTKAQLGL

Parental  ELEELEAAALLVQEEETALKAAHSVSGQQTLCSSSEASDSEDSDSSVSSGNEDSGSDSEQDELKDSPSET
          ELEELEAAALLVQEEE.AL.AAHSVSGQQ.LC.SSEA.DSEDSDS.VSSGNEDS.S.SEQDELKDSPSET
Retrocopy ELEELEAAALLVQEEESALQAAHSVSGQQKLCCSSEAGDSEDSDSTVSSGNEDSDSHSEQDELKDSPSET

Parental  VSSLQGPF-LEESSAFLIVDGGVRRNTAIQESDASQGKPLASSWPLGVSGPLIEELGEQLKTTVQVSEPK
          V.....PF.LEESSA.LIVDGGV.RNTAIQESDASQGKPLASS.PLGVSGPLIEELGEQLKTTVQV.EP.
Retrocopy V-LCKVPF<LEESSALLIVDGGVCRNTAIQESDASQGKPLASSRPLGVSGPLIEELGEQLKTTVQVFEPE

Parental  GTTAVNRSNIQERDGCQTPN
          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	0.21 RPM	6.38 RPM
SRP007412_cerebellum	1.04 RPM	6.70 RPM
SRP007412_heart	0.17 RPM	6.97 RPM
SRP007412_kidney	1.15 RPM	11.79 RPM
SRP007412_liver	0.62 RPM	6.55 RPM
SRP007412_testis	2.74 RPM	10.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_486 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_486 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_486 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_674
Gorilla gorilla	retro_ggor_581

---

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 ,