RetrogeneDB ID: retro_hsap_1566

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:49657321..49658881(-)
• Located in intron of: ENSG00000156958

Retrocopy information

• Ensembl ID: ENSG00000259531
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SPPL2A
• Ensembl ID: ENSG00000138600
• Aliases: SPPL2A, IMP3, PSL2
• Description: signal peptide peptidase like 2A [Source:HGNC Symbol;Acc:30227]

Sequence

>retro_hsap_1566
ATGGGGCCGCAGCGGCGGCTGTCCCCTGCCACGGCCGCCCTGCTCTGGGGCTTCCTGCTCCAGCTGACAGCCGCTCAGGA
AGCAATCTTGCATGCGTCTGGAAATGGCACATCCAAGGACTACTGCATGCTTTATAACCCCCATTGGTCAGCTCTTCCAA
GTACCCTAGAAAATGCAACTTCCATTAGTTTGATGAATCTGACTTCCGCACCACTATGCAACCTTTCTGATGTTCCTCCT
GTTGACATAAAGAACAAAGCAGTTGTGGTGCAATGGGGCAGCTGCCATTTTCTTGAAAACACCAGAAATGCACAGAAAAG
AGGTGCTGAAGCAATGTTGGTTGTCAATAACAGTATCCTATTTCCTACCTCAGGTAACAGATCTGAATTTCCTGATGTGA
AAATACTGATTGCATTTATAAGTGACAAAGACTTTATAGATATGAAGCAGACTCTAGGAAATAACATTACTGTGAAAATG
TGTTCTCCATCGTGGCCTAACTTTGATTATACTATGGTGGTTATTTTTGTAATTGCTGTGTTCACTGTGGCATTAGGTGG
ATACTGGAGTGGACTAGTTGAATTGGAAAACTTGAAAGCAGTGACAACTGAAGATAGATAAATGAGGGAAAAAAAAGGAA
GAATATCTAACTTTTAGTCCTCTTACAGTTGTAATATTTGTAGTCATCTACTGTGTTATGATGGTCTTACTTTATTTCTT
CCACAAATGGTTAGTTTATGTTATGATAGCAATTTTCTGCATAGTATCAGCAATGAGTCTGTACAACTCTCTTGCTGCAC
TAATTCATAAGATGCCATATGGACAATGCACAATTGAGTGTCGCGGCAAAAGCATGGAAGTGAGACTTATGTTTCTCTCT
GGACTGTGCATAGCAATAGCTATTGTTTGGGCTGTGTTTCAAAATGAAGACAGGTGGGCTTGGATTTTACAAGATATCTT
GGAGATTGCTTTCTGTCTGAATTTAATTAAAACACTGAAGTTGGCCAGCTTCAAGTCATGTGTGATACTTCTAGGCCTTC
TCCTCCTCTATGATGTATTTTTTGTTTTCATAACACCATTCATCACAAAGAATGGTGAGAGTATCATGGTTAAACTTGCA
GCTGGACCTTTTGAAAATACTGAAACATTGCCAGTAGTCATCAGAGTACCAAAGCTGATCTGTTTCTCAGTAATGAGTGT
GTGCATCATGCCTGTTTCAATATTGGGCTTTGGAGACATTATTGTACAGGCCTGTTGCTTGCGTACTGTAGAAGAGTTGA
TGTTTAGACTGGTTCTTCGTATATATACTATGTTTCCTCTACAGTTGCCTATGCTATTGGCATGATACTTACATTTGTTG
TTCTGGTGCTGATGAAAAAGGGGCAACCTGCTCTCCTCTATTTAGTAACTTGCACACTTATTATTGCCTCAGTTGTTGCC
TGGAAATGTAAGGAAATGAAAAAGTTCTGGAAAGGTAACAGCTATCAGATGATGGACCATCTGTATTATGCAAAAAACGA
AGAAAACCCTGTGATGTCTGGTGAACAGATTGTCCAGCAA

Alignment

ORF - retro_hsap_1566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGPQRRLSPAGAALLWGFLLQLTAAQEAILHASGNGTTKDYCMLYNPYWTALPSTLENATSISLMNLTST
          MGPQRRLSPA.AALLWGFLLQLTAAQEAILHASGNGT.KDYCMLYNP.W.ALPSTLENATSISLMNLTS.
Retrocopy MGPQRRLSPATAALLWGFLLQLTAAQEAILHASGNGTSKDYCMLYNPHWSALPSTLENATSISLMNLTSA

Parental  PLCNLSDIPPVGIKSKAVVVPWGSCHFLEKARIAQKGGAEAMLVVNNSVLFPPSGNRSEFPDVKILIAFI
          PLCNLSD.PPV.IK.KAVVV.WGSCHFLE..R.AQK.GAEAMLVVNNS.LFP.SGNRSEFPDVKILIAFI
Retrocopy PLCNLSDVPPVDIKNKAVVVQWGSCHFLENTRNAQKRGAEAMLVVNNSILFPTSGNRSEFPDVKILIAFI

Parental  SYKDFRDMNQTLGDNITVKMYSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDREMR-
          S.KDF.DM.QTLG.NITVKM.SPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDR.MR.
Retrocopy SDKDFIDMKQTLGNNITVKMCSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDR*MR>

Parental  KKKEEYLTFSPLTVVIFVVICCVMMVLLYFFYKWLVYVMIAIFCIASAMSLYNCLAALIHKIPYGQCTIA
          ...EEYLTFSPLTVVIFVVI.CVMMVLLYFF.KWLVYVMIAIFCI.SAMSLYN.LAALIHK.PYGQCTI.
Retrocopy XXXEEYLTFSPLTVVIFVVIYCVMMVLLYFFHKWLVYVMIAIFCIVSAMSLYNSLAALIHKMPYGQCTIE

Parental  CRGKNMEVRLIFLSGLCIAVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLL
          CRGK.MEVRL.FLSGLCIA.A.VWAVF.NEDRWAWILQDIL.IAFCLNLIKTLKL..FKSCVILLGLLLL
Retrocopy CRGKSMEVRLMFLSGLCIAIAIVWAVFQNEDRWAWILQDILEIAFCLNLIKTLKLASFKSCVILLGLLLL

Parental  YDVFFVFITPFITKNGESIMVELAAGPFGNNEKLPVVIRVPKLIYFSVMSVCLMPVSILGFGDIIV-PGL
          YDVFFVFITPFITKNGESIMV.LAAGPF.N.E.LPVVIRVPKLI.FSVMSVC.MPVSILGFGDIIV..GL
Retrocopy YDVFFVFITPFITKNGESIMVKLAAGPFENTETLPVVIRVPKLICFSVMSVCIMPVSILGFGDIIV<TGL

Parental  LIAYCRRFDVQTGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLVPCTLITASVVAWRRKEMKK
          L.AYCRR.DV.TGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLV.CTLI.ASVVAW..KEMKK
Retrocopy LLAYCRRVDV*TGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLVTCTLIIASVVAWKCKEMKK

Parental  FWKGNSYQMMDHLDCATNEENPVISGEQIVQQ
          FWKGNSYQMMDHL..A.NEENPV.SGEQIVQQ
Retrocopy FWKGNSYQMMDHLYYAKNEENPVMSGEQIVQQ

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
bodymap2_adipose	0.08 RPM	56.93 RPM
bodymap2_adrenal	0.02 RPM	60.45 RPM
bodymap2_brain	0.00 RPM	15.45 RPM
bodymap2_breast	0.06 RPM	60.16 RPM
bodymap2_colon	0.00 RPM	34.98 RPM
bodymap2_heart	0.06 RPM	57.41 RPM
bodymap2_kidney	0.62 RPM	72.73 RPM
bodymap2_liver	0.08 RPM	49.39 RPM
bodymap2_lung	0.00 RPM	45.38 RPM
bodymap2_lymph_node	0.22 RPM	28.93 RPM
bodymap2_ovary	0.21 RPM	38.65 RPM
bodymap2_prostate	0.12 RPM	32.72 RPM
bodymap2_skeletal_muscle	0.16 RPM	158.58 RPM
bodymap2_testis	0.00 RPM	34.88 RPM
bodymap2_thyroid	0.04 RPM	74.76 RPM
bodymap2_white_blood_cells	0.00 RPM	63.24 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1566 was not detected

EST

No EST(s) were mapped for retro_hsap_1566 retrocopy.

TSS

No TSS is located nearby retro_hsap_1566 retrocopy 5' end.

Lab

retro_hsap_1566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1566 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1054
Gorilla gorilla	retro_ggor_1191
Pongo abelii	retro_pabe_1293

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000008946	1 retrocopy	retro_dord_754,
Homo sapiens	ENSG00000138600	1 retrocopy	retro_hsap_1566 ,
Homo sapiens	ENSG00000157837	1 retrocopy	retro_hsap_1898,
Gorilla gorilla	ENSGGOG00000013154	1 retrocopy	retro_ggor_1191,
Pongo abelii	ENSPPYG00000006472	1 retrocopy	retro_pabe_1293,
Pan troglodytes	ENSPTRG00000007070	1 retrocopy	retro_ptro_1054,
Rattus norvegicus	ENSRNOG00000011652	1 retrocopy	retro_rnor_1750,