RetrogeneDB ID: retro_pabe_3459

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:27296433..27297675(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERPINH1
• Ensembl ID: ENSPPYG00000003691
• Aliases: None
• Description: serpin H1 precursor [Source:RefSeq peptide;Acc:NP_001125445]

Sequence

>retro_pabe_3459
CGCTCCCTCCTGCTCCTCAGCGCCTTCTGCCTCCTGGCAGTGGCCTTGGCGACCGAGGTGAAGAAACCTGCAGCCACAGC
AGCTCCTGGCACCGCAGAGAAGCTGAGCCCCAAGGCAGCCACGCTGGCCGAACACAGCGCCAGCCTGGCCTTCAGCCTGT
ACCAGGACATGGCCAAGGACCAGGTGGTGGAGAACATCCTGGTGTCGCCCGTGGTGGTAGCCTCGTCGCTGGGGCTCGTG
TCGCTGGGCGGCCAGGCGACCACGGCGTCGCAGGCCAAGGCAGTGCTGAGCGCCAAGCAGCTGCGCGACTAGGAGGTGCA
CGCCGCCGTGGGCGAGCCGTTGCGCTCACTCAGCAACTCCACCGCGCGCAACGTGACCTGGAAGCTGGGCAGCCGCCTGT
AGGGACCCAGCTCAGTGAGTTTCACTGATGACTTCGTGCGCAGCAGCAAGCAGCACTACAACTGCGAGCACTCCAAGATC
AATTTCCATGACAAGTGCAGCGCGCTGCAGTCCATCCACGAGTGGGCCGCACAGACCACCAACGGCAAGCTGCCCGAGGT
CACCAAGGACATGGAGTGCATGGATGGCGTCCTGCTTGTCAACGCCATGTTCTTCAAGCCACACTGGAATGAGAAATTCC
ACCACAAGATGGTGGAAAACCATGGCTTCATGGTGACTCGGTTCTATACCGTGGGTGTCATGATGATGCACCAGACAGGC
CTCTACAACTACTTTGACAACGAGAAGGAAAAGCTGCAAATCGTGGAGATGCCCCTGGTCCACAAGCTCTCCAGCCTCAT
CATCCTCATGCCCTACCACGTGGACCCCTCCAGGCCTTAAAAAGCTGCTAACCAAAGAGCAGCTGAAGATCTGGATGGGG
AAGAAGCAGAAGGCTGTCGCCATCTCCTTGCCCAAGGGTGTGGTGGAGGTTCCCATGACCTGCAGAAACTCCTGGCTGGG
CTTGGCCTGACTGAGGCCATTGACAAGAACAAGGCAAACTTGTCACGCATGCCACGCAAGAAGGACCTATACCTGACCAG
CGTGTTCCATGCCACCGCCTTTGAGTTGGACACAGACGGCAACTCCTTTGACCAGGACATCTATGGGAGCGAGGAGCTGC
GAAGCCCCAAGCTGTTCTACTCCGACCACCCCTTCATCTTCCTGGTGTGGGACACCCAGAGCGGCTCCCTGCTGTTCACT
GGGCGCCTGGTGCGGCCTAAGGTTGACAAGATGCAAGATGAG

Alignment

ORF - retro_pabe_3459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.11 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RSLLLLSAFCLLAAALAAEVKKPAAAAAPGTAEKLSPKAATLAERSAGLAFSLYQAMAKDQAVENILVSP
          RSLLLLSAFCLLA.ALA.EVKKPAA.AAPGTAEKLSPKAATLAE.SA.LAFSLYQ.MAKDQ.VENILVSP
Retrocopy RSLLLLSAFCLLAVALATEVKKPAATAAPGTAEKLSPKAATLAEHSASLAFSLYQDMAKDQVVENILVSP

Parental  VVVASSLGLVSLGGKATTASQAKAVLSAEQLRDEEVHAGLGELLRSLSNSTARNVTWKLGSRLYGPSSVS
          VVVASSLGLVSLGG.ATTASQAKAVLSA.QLRD.EVHA..GE.LRSLSNSTARNVTWKLGSRL.GPSSVS
Retrocopy VVVASSLGLVSLGGQATTASQAKAVLSAKQLRD*EVHAAVGEPLRSLSNSTARNVTWKLGSRL*GPSSVS

Parental  FADDFVRSSKQHYNCEHSKINFRDKRSALQSINEWAAQTTDGKLPEVTKDVERTDGALLVNAMFFKPHWD
          F.DDFVRSSKQHYNCEHSKINF.DK.SALQSI.EWAAQTT.GKLPEVTKD.E..DG.LLVNAMFFKPHW.
Retrocopy FTDDFVRSSKQHYNCEHSKINFHDKCSALQSIHEWAAQTTNGKLPEVTKDMECMDGVLLVNAMFFKPHWN

Parental  EKFHHKMVDNRGFMVTRSYTVGVMMMHRTGLYNYYDDEKEKLQIVEMPLAHKLSSLIILMPHHVE-PLER
          EKFHHKMV.N.GFMVTR.YTVGVMMMH.TGLYNY.D.EKEKLQIVEMPL.HKLSSLIILMP.HV..PL..
Retrocopy EKFHHKMVENHGFMVTRFYTVGVMMMHQTGLYNYFDNEKEKLQIVEMPLVHKLSSLIILMPYHVD<PLQA

Parental  LE-KLLTKEQLKIWMGKMQKKAVAISLPKGVVEV-THDLQKHLAGLGLTEAIDKNKADLSRMSGKKDLYL
          L..KLLTKEQLKIWMGK.Q.KAVAISLPKGVVEV..HDLQK.LAGLGLTEAIDKNKA.LSRM..KKDLYL
Retrocopy LK<KLLTKEQLKIWMGKKQ-KAVAISLPKGVVEV<SHDLQKLLAGLGLTEAIDKNKANLSRMPRKKDLYL

Parental  ASVFHATAFELDTDGNPFDQDIYGREELRSPKLFYADHPFIFLVRDTQSGSLLFIGRLVRPKGDKMRDE
          .SVFHATAFELDTDGN.FDQDIYG.EELRSPKLFY.DHPFIFLV.DTQSGSLLF.GRLVRPK.DKM.DE
Retrocopy TSVFHATAFELDTDGNSFDQDIYGSEELRSPKLFYSDHPFIFLVWDTQSGSLLFTGRLVRPKVDKMQDE

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	16.81 RPM
SRP007412_cerebellum	0.00 RPM	11.43 RPM
SRP007412_heart	0.00 RPM	48.32 RPM
SRP007412_kidney	0.00 RPM	93.67 RPM
SRP007412_liver	0.00 RPM	64.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3459 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3459 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 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,
Pongo abelii	ENSPPYG00000006108	1 retrocopy	retro_pabe_253,
Pan troglodytes	ENSPTRG00000004083	1 retrocopy	retro_ptro_2822,