RetrogeneDB ID: retro_hsap_2554

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 22:30938559..30940067(+)
• Located in intron of: ENSG00000214491

Retrocopy information

• Ensembl ID: ENSG00000225774
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SIRPA
• Ensembl ID: ENSG00000198053
• Aliases: SIRPA, BIT, CD172A, MFR, MYD-1, P84, PTPNS1, SHPS1, SIRP
• Description: signal-regulatory protein alpha [Source:HGNC Symbol;Acc:9662]

Sequence

>retro_hsap_2554
ATGGAGCCCGCGGGCCGGTCCCCGGCCGCCTCGGGCCGCTGCTCTGCCTGCTGCTCCCCGCGTCCTGCGCCTGGTCAGGA
GTGGCGGGTGAGGAGGAGCTGCAGGTGATTCAGCCTGAGAAGTCTGTATCAGTTGCAGCTGGAGAGTCGGCCGCTCTGCA
GTGCACTGTGACCTCCCTGAACCCTGTGGGGCCCATCCAACGGTTCAGAGGAGCTGGACCAGGCCGGAAATTAATCTACC
ATCAAAAAGAAGGCCACTTCCCCCGGGTAACAACTGTTTCAGATCTCACAAAGAGAACCAACATGGACTTTTCCATCTGC
ATCAGTAACATCACCCCAGCAGATGCCGGCACCTACTACTGTGTGAAGTTCCAGAAAGGGAGCCCTGACGTGGAGTTGAA
GTCTGGAGCAGGCACTGAGCTGTCTGTGCGTGCCAAACCCTCTGCCCCCGTGGTATCGGGCCCCGCAGCGAGGGCCACAC
CTGACCACACAGTGAGCTTCACCTGCGAGTCTCATGGCTTCTCACCCAGAGACATCAGCCTGAAATGGTTCAAAAATGGG
AATCAGCTCTCAGACTTCCAGACCAACGTGGACCCCGCAAGAGAGAGCGTGTCCTACAGCATCCACAGCACAGCCAATGT
GGTGCTGACCCGCGGGGACATTCACTCTCAAGTCATCTGCGAGGTGGCCCACGTCACCTTGCGGGGGGACTCTTTTCGTG
GGACTGCCAACTTGTCTGAGACTATCCAAGTTCCACCCACCTTGGAGGTTACTCAACAGCCCATGAGGGCAGAGAACCAG
GTGAATATCACCTGCCAGGTGACGAAATTCTACCCCCAGAGACTACAGTTGACCTGGTTGGAGAACGGCAATGTGTCCCG
GACAGAAACGGCCTCAACTCTTACAGAGAACAAGGATGGCACCTACAACTGGATGAGCTGGCTCCTGGTGAATGTATCTG
CCCACAGGGATGATGTGAAGCTCACCTGCCAGGTGGAGCATGACGGGCAGTCAGCGGTCAGCAAAAGCCATGACCTGAAG
GTCTCAGCCCACCTGAAGGAGCAGAGCTCAAATACCGCCGCTGAGAACACTGGACCTAATGAACAGAACATCTATATTGT
GGTGGGCGTGGTGTGCACCTTGCTGGTGGCCCTACTGATGGAGGCTCTCTACCTCGTCCGAATCAGACAGAAGAAAGCCC
AGGGCTCCACTTCTTCTACAAGGTTGCATGAACCCGAGAAGAATGCCAGAAAAATAACCCAGGACACAAATGATATCACA
TATGCGGACCTGAACCTGCCCAAGGGGAAGAAGCCTGCTCCCCGGGCCGCGGAGCCCAACAACCACACAGAGTATGCCAG
CATTCAGACCAGCCTGCAGCCTGCGTCGGAGGACACCCTCACCTATGCTGACCTGGACATGGTGCACCTCAACCGGACCC
CCAAGCAGCTGGCCCCCAAGCCCGAGCTGTCCTTCTCAGAGTATGCCAGCATCCAGGTCCCGAGGAAG

Alignment

ORF - retro_hsap_2554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.69 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEPAG-PAPGRLGPLLCLLLAASCAWSGVAGEEELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWF
          MEPAG.P.PGRLGPLLCLLL.ASCAWSGVAGEEELQVIQP.KSV.VAAGE.A.L.CT.TSL.PVGPIQ.F
Retrocopy MEPAG<PVPGRLGPLLCLLLPASCAWSGVAGEEELQVIQPEKSVSVAAGESAALQCTVTSLNPVGPIQRF

Parental  RGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRIGNITPADAGTYYCVKFRKGSPDDVEFKSGAG
          RGAGPGR.LIY.QKEGHFPRVTTVSDLTKR.NMDFSI.I.NITPADAGTYYCVKF.KGSPD.VE.KSGAG
Retrocopy RGAGPGRKLIYHQKEGHFPRVTTVSDLTKRTNMDFSICISNITPADAGTYYCVKFQKGSPD-VELKSGAG

Parental  TELSVRAKPSAPVVSGPAARATPQHTVSFTCESHGFSPRDITLKWFKNGNELSDFQTNVDPVGESVSYSI
          TELSVRAKPSAPVVSGPAARATP.HTVSFTCESHGFSPRDI.LKWFKNGN.LSDFQTNVDP..ESVSYSI
Retrocopy TELSVRAKPSAPVVSGPAARATPDHTVSFTCESHGFSPRDISLKWFKNGNQLSDFQTNVDPARESVSYSI

Parental  HSTAKVVLTREDVHSQVICEVAHVTLQGDPLRGTANLSETIRVPPTLEVTQQPVRAENQVNVTCQVRKFY
          HSTA.VVLTR.D.HSQVICEVAHVTL.GD..RGTANLSETI.VPPTLEVTQQP.RAENQVN.TCQV.KFY
Retrocopy HSTANVVLTRGDIHSQVICEVAHVTLRGDSFRGTANLSETIQVPPTLEVTQQPMRAENQVNITCQVTKFY

Parental  PQRLQLTWLENGNVSRTETASTVTENKDGTYNWMSWLLVNVSAHRDDVKLTCQVEHDGQPAVSKSHDLKV
          PQRLQLTWLENGNVSRTETAST.TENKDGTYNWMSWLLVNVSAHRDDVKLTCQVEHDGQ.AVSKSHDLKV
Retrocopy PQRLQLTWLENGNVSRTETASTLTENKDGTYNWMSWLLVNVSAHRDDVKLTCQVEHDGQSAVSKSHDLKV

Parental  SAHPKEQGSNTAAENTGSNERNIYIVVGVVCTLLVALLMAALYLVRIRQKKAQGSTSSTRLHEPEKNARE
          SAH.KEQ.SNTAAENTG.NE.NIYIVVGVVCTLLVALLM.ALYLVRIRQKKAQGSTSSTRLHEPEKNAR.
Retrocopy SAHLKEQSSNTAAENTGPNEQNIYIVVGVVCTLLVALLMEALYLVRIRQKKAQGSTSSTRLHEPEKNARK

Parental  ITQDTNDITYADLNLPKGKKPAPQAAEPNNHTEYASIQTSPQPASEDTLTYADLDMVHLNRTPKQPAPKP
          ITQDTNDITYADLNLPKGKKPAP.AAEPNNHTEYASIQTS.QPASEDTLTYADLDMVHLNRTPKQ.APKP
Retrocopy ITQDTNDITYADLNLPKGKKPAPRAAEPNNHTEYASIQTSLQPASEDTLTYADLDMVHLNRTPKQLAPKP

Parental  EPSFSEYASVQVPRK
          E.SFSEYAS.QVPRK
Retrocopy ELSFSEYASIQVPRK

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	0.16 RPM	170.95 RPM
bodymap2_adrenal	0.00 RPM	68.98 RPM
bodymap2_brain	0.09 RPM	204.49 RPM
bodymap2_breast	0.04 RPM	65.29 RPM
bodymap2_colon	0.00 RPM	48.75 RPM
bodymap2_heart	0.00 RPM	22.41 RPM
bodymap2_kidney	0.21 RPM	46.57 RPM
bodymap2_liver	0.09 RPM	59.57 RPM
bodymap2_lung	0.11 RPM	74.79 RPM
bodymap2_lymph_node	0.07 RPM	84.84 RPM
bodymap2_ovary	0.06 RPM	58.68 RPM
bodymap2_prostate	0.26 RPM	50.54 RPM
bodymap2_skeletal_muscle	0.00 RPM	35.87 RPM
bodymap2_testis	0.26 RPM	36.12 RPM
bodymap2_thyroid	0.04 RPM	20.77 RPM
bodymap2_white_blood_cells	0.79 RPM	230.74 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_2554 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CKX	POLR2A	22:30938415..30938835
ENCFF002CMI	POLR2A	22:30938433..30938803
ENCFF002DBE	POLR2A	22:30938385..30938881

EST

No EST(s) were mapped for retro_hsap_2554 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_107720	734 libraries	481 libraries	407 libraries	102 libraries	105 libraries

The graphical summary, for retro_hsap_2554 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_2554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2554 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000198053	1 retrocopy	retro_hsap_2554 ,
Sorex araneus	ENSSARG00000013888	1 retrocopy	retro_sara_435,