RetrogeneDB ID: retro_ptro_2822

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:34730715..34731958(+)
• Located in intron of: ENSPTRG00000020874

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERPINH1
• Ensembl ID: ENSPTRG00000004083
• Aliases: None
• Description: Pan troglodytes serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1) (SERPINH1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246610]

Sequence

>retro_ptro_2822
CGCTCCCTCCTGCTCCTCAGTGCCTTCTGCCTCCTGGCGGTGGCCTTGGCGACCGAGGTGAAGAAACCTGCAGCCACAGC
AGCTCCTGGCACCGCAGAGAAGCTGAGCCCCAAGGCAGCCACGCTGGCCGAACACAGCGCCGGCCTGGCCTTCAGCCTGT
ACCAGGCCATGGCCAAGGACCAGGCGGTGGAGAACATCCTGGTGTCGCCCGTGGTGGTGGCCTCGTCGCTGGGGCTCGTG
TCGCTGGGCGGCAAGGCGACCACGGCGTCGGAGGCCAAGGCAGTGCTGAGTGCCAAGCAGCTGCGCGACGAGGAGGTGCA
CGCCGGCGTGGGCGAGCTGCTGCGTTCACTCAGCAACTCCACCGCGCGCAACGTGACCTGGAAGCTGTGCAGTCGCCTGT
AGGGACCCAGCTCAGTGAGTTTCGCTGATGACTTCGTGCGCAGCAGCAAGCAGCACTACAACTGCGAGCACTCCAAGATC
AATTTCCATGACAAGTGCAGTCCGCTGCAGTCCATCCACGAGTGGGCCGTGCAGACCACCGACGGCAAGCTGCCCAAGGT
CACCAAGGACATGGAGTGCATGGATGGCGCCCTGCTTGTCAACACCATGTTCTTCAAGCCACACTGGAATGAGAAATTCC
ACCACAAGATGGTGGAAAACCGTGGCTTCATGGTGACTCGGTTCTATACCGTGGGTGTCATGGTGATGCACCAGACAGGC
CTCTACAACTACTATGACAATGAGAAGGAAAAGCTGCAAATTGTGGAGATGCCCCTGGCCCACAAGCTCTCCAGCCTCAT
CATCCTCATGCCCCACCACGTGGAGCCCCTCGAGGCCTTAAAAAGCTGCTAACCAAAGAGCAGCTGAAGATCTGGATGGG
GAAGAAGCAGAAGCCTGTCGCCATCTCCTTGCCCAAGCGGGTGGTGGAAGTTCCCATGACCTGCAGAAACTCCTGGCTGG
GCTTGGCCTGACTGAGGCCATTGACAAGAACAAGGCAAACTTGTCACGCATGCCACACAAGAAGGACCTGTACCTGACCA
GCGTGTTCCACGCCACCGCCTTTGAGTTGGACACAGACGGCAACTCCTTTGACCAGGACATCTATGGGAGCAAGGAGCTG
CGCAGCCCCAAGCTGTTCTACTCCGACCACGCCTTCATCTTCCTGGTGTGGGACACCCAGAGCGGCTCCCTGCTGTTCAC
TGGGTACCTGGTCCGGCCTAAGGTTGACAAGATGCGAGACGAG

Alignment

ORF - retro_ptro_2822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSLLLLSAFCLLEAALAAEVKKPAAAAAPGTAEKLSPKAATLAERSAGLAFSLYQAMAKDQAVENILVSP
          RSLLLLSAFCLL..ALA.EVKKPAA.AAPGTAEKLSPKAATLAE.SAGLAFSLYQAMAKDQAVENILVSP
Retrocopy RSLLLLSAFCLLAVALATEVKKPAATAAPGTAEKLSPKAATLAEHSAGLAFSLYQAMAKDQAVENILVSP

Parental  VVVASSLGLVSLGGKATTASQAKAVLSAEQLRDEEVHAGLGELLRSLSNSTARNVTWKLGSRLYGPSSVS
          VVVASSLGLVSLGGKATTAS.AKAVLSA.QLRDEEVHAG.GELLRSLSNSTARNVTWKL.SRL.GPSSVS
Retrocopy VVVASSLGLVSLGGKATTASEAKAVLSAKQLRDEEVHAGVGELLRSLSNSTARNVTWKLCSRL*GPSSVS

Parental  FADDFVRSSKQHYNCEHSKINFRDKRSALQSINEWAAQTTDGKLPEVTKDVERTDGALLVNAMFFKPHWD
          FADDFVRSSKQHYNCEHSKINF.DK.S.LQSI.EWA.QTTDGKLP.VTKD.E..DGALLVN.MFFKPHW.
Retrocopy FADDFVRSSKQHYNCEHSKINFHDKCSPLQSIHEWAVQTTDGKLPKVTKDMECMDGALLVNTMFFKPHWN

Parental  EKFHHKMVDNRGFMVTRSYTVGVMMMHRTGLYNYYDDEKEKLQIVEMPLAHKLSSLIILMPHHVEPLER-
          EKFHHKMV.NRGFMVTR.YTVGVM.MH.TGLYNYYD.EKEKLQIVEMPLAHKLSSLIILMPHHVEPLE..
Retrocopy EKFHHKMVENRGFMVTRFYTVGVMVMHQTGLYNYYDNEKEKLQIVEMPLAHKLSSLIILMPHHVEPLEA<

Parental  LEKLLTKEQLKIWMGKMQKKAVAISLPKGVVEV-THDLQKHLAGLGLTEAIDKNKADLSRMSGKKDLYLA
          L.KLLTKEQLKIWMGK.Q.K.VAISLPK.VVEV..HDLQK.LAGLGLTEAIDKNKA.LSRM..KKDLYL.
Retrocopy LKKLLTKEQLKIWMGKKQ-KPVAISLPKRVVEV<SHDLQKLLAGLGLTEAIDKNKANLSRMPHKKDLYLT

Parental  SVFHATAFELDTDGNPFDQDIYGREELRSPKLFYADHPFIFLVRDTQSGSLLFIGRLVRPKGDKMRDE
          SVFHATAFELDTDGN.FDQDIYG..ELRSPKLFY.DH.FIFLV.DTQSGSLLF.G.LVRPK.DKMRDE
Retrocopy SVFHATAFELDTDGNSFDQDIYGSKELRSPKLFYSDHAFIFLVWDTQSGSLLFTGYLVRPKVDKMRDE

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	0.05 RPM	12.71 RPM
SRP007412_cerebellum	0.11 RPM	4.77 RPM
SRP007412_heart	0.00 RPM	34.48 RPM
SRP007412_kidney	0.16 RPM	69.69 RPM
SRP007412_liver	0.00 RPM	28.61 RPM
SRP007412_testis	0.53 RPM	12.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2822 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2822 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2822 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4151

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000149257	1 retrocopy	retro_hsap_4151,
Macaca mulatta	ENSMMUG00000007675	1 retrocopy	retro_mmul_1180,
Nomascus leucogenys	ENSNLEG00000016882	1 retrocopy	retro_nleu_1389,
Pongo abelii	ENSPPYG00000003691	2 retrocopies	retro_pabe_3459, retro_pabe_3514,
Pan troglodytes	ENSPTRG00000004083	1 retrocopy	retro_ptro_2822 ,