RetrogeneDB ID: retro_hsap_3048

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:69862655..69863427(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000250277
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSG00000144228
• Aliases: SPOPL, BTBD33
• Description: speckle-type POZ protein-like [Source:HGNC Symbol;Acc:27934]

Sequence

>retro_hsap_3048
AAATTCATTAGAAGGGACCATTTGCTTGACGAAGCTGAAGGTCTTTTACCAGATGACGAGCTTACATTATTTTGTGAGAT
GAGTGTGGTACTAGATTCAGTAAACATATCAGGACATACTAATACAAATACTTTGAAGGTGGCTGAGTGTCGACTAGGAG
AAGATTTATGTAATCTCTGTGAAAACACAAGATGTACAGACTGTAGTTTTTTGTGAGAGGACAAGAATTTAAAGCTCATA
AATCTGCTGGTACCTCCATCCCCAGTTTTTAATGCCATGTTTGAACATGAAATGGAAGAAAACATAAAGAATCGAGTGGA
AATAAATTATTTAGGCCCTGATGTTTTTAAAGAAATGATGAGATTCATTAACACAGGGAAATAACTAAACCTTGACAAAA
TGGCTGACAACTTGTTGGCAGCTGCAGACAAACATGCACTGGGAACAGCTGAAAGTCATGTGTGAGGAAGCTTTGTGTAG
TAATCCCTCAGTAGAAAATGTTGTTGATACACTTGTCCTTGCAGATTTGCACATTGCAGAACAGTTGAAAGCAAAAGCCA
TAGACATTATTAGTAGGTGCAGTGTACTTCGACAACTTGGGTGTAAACATAAGAAAAACTGGAACAGCAACCAAGCAACC
GACATAATGGAAACATCAAGGTGGAAGTCCATGATTCAGTCTCACTCTTACTTAGCAGCAGAAGCCTTCTGAGCACTAGC
ATCTGCACAGTGTCCACAGTTTGGCATTCCACACACACGGCTAAAACAGTCC

Alignment

ORF - retro_hsap_3048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.38 %
• Parental protein coverage: 65.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KFIRRDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDCS-
          KFIRRD.LLDEA.GLLPDD.LTLFCE.SVV.DSVNISGHTNTNTLKV.ECRL.EDL.NL.ENTR.TDCS.
Retrocopy KFIRRDHLLDEAEGLLPDDELTLFCEMSVVLDSVNISGHTNTNTLKVAECRLGEDLCNLCENTRCTDCS<

Parental  FFVRGQEFKAHKSVLAARSPVF-NAMFEHEMEESKKNRVEINDLDPEVFKEMMRFIYTGRAPNLDKMADN
          FFVRGQEFKAHKS......P.F.NAMFEHEMEE..KNRVEIN.L.P.VFKEMMRFI.TG...NLDKMADN
Retrocopy FFVRGQEFKAHKSA-GTSIPSF>NAMFEHEMEENIKNRVEINYLGPDVFKEMMRFINTGK*LNLDKMADN

Parental  LLAAADKYAL-ERLKVMCEEALCSNLSVENVADTLVLADLHSAEQLKAQAIDFINRCSVLRQLGCKDGKN
          LLAAADK.AL.E.LKVMCEEALCSN.SVENV.DTLVLADLH.AEQLKA.AID.I.RCSVLRQLGCK..KN
Retrocopy LLAAADKHAL>EQLKVMCEEALCSNPSVENVVDTLVLADLHIAEQLKAKAIDIISRCSVLRQLGCKHKKN

Parental  WNSNQATDIMETSGWKSMIQSHPHLVAEAFRALASAQCPQFGIPRKRLKQS
          WNSNQATDIMETS.WKSMIQSH..L.AEAF.ALASAQCPQFGIP..RLKQS
Retrocopy WNSNQATDIMETSRWKSMIQSHSYLAAEAF*ALASAQCPQFGIPHTRLKQS

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	0.00 RPM	44.53 RPM
bodymap2_adrenal	0.00 RPM	30.19 RPM
bodymap2_brain	0.00 RPM	40.57 RPM
bodymap2_breast	0.00 RPM	45.12 RPM
bodymap2_colon	0.00 RPM	64.97 RPM
bodymap2_heart	0.00 RPM	27.89 RPM
bodymap2_kidney	0.00 RPM	36.94 RPM
bodymap2_liver	0.00 RPM	14.45 RPM
bodymap2_lung	0.00 RPM	51.48 RPM
bodymap2_lymph_node	0.00 RPM	47.53 RPM
bodymap2_ovary	0.00 RPM	42.76 RPM
bodymap2_prostate	0.00 RPM	59.08 RPM
bodymap2_skeletal_muscle	0.00 RPM	14.19 RPM
bodymap2_testis	0.00 RPM	37.95 RPM
bodymap2_thyroid	0.00 RPM	35.74 RPM
bodymap2_white_blood_cells	0.00 RPM	140.28 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3048 was not detected

EST

No EST(s) were mapped for retro_hsap_3048 retrocopy.

TSS

No TSS is located nearby retro_hsap_3048 retrocopy 5' end.

Lab

retro_hsap_3048 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3048 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048 ,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440, retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054,