RetrogeneDB ID: retro_hsap_2822

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:103257951..103258872(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000240107
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSX2IP
• Ensembl ID: ENSG00000117155
• Aliases: SSX2IP, ADIP
• Description: synovial sarcoma, X breakpoint 2 interacting protein [Source:HGNC Symbol;Acc:16509]

Sequence

>retro_hsap_2822
AGACAGTTACAATGCAAGAACAGGAATTTGAATCAGCTATTGAAAAATGAGAAGGATAAGGTACAGAAATTACGAAATAT
TATTGTAAGTTGAGCTATTCAGTATTATCATGATATGATATGAAAAGAGTGTGAATATAACAAACTGAAGGAAAGTCTAC
ATCAACCTTTTATGAACCAAAAAGAATTAAAAATAGCTTTAGACATTTTAAATAATGTGGGGAGAGCTGATGGAAAAAGA
GGCCTCTGGAAAACTGGTAAGACAGAAGTCAGGAATTTGATGAAATGTATAAAATTATCTTGAATGATTATGAGTATTGT
CACAAACAATTCCTAATGGAAAATGCTGATAATGAAGAAGTTTCTTCACCAAATGGAAAAGGATATGTTTTTTCTTCTTT
CTCCTCAAAAGAAACCTAGAGAAAGAGAAGATGGTAGTACAGGAACTGTTATCTCAGATGTTGAAGAAGATGCTGGGGAA
ATGAGCAGAGACAGTATCTGGGAACTTTCCTGTGAAACTGTGAGAGAACAGCCTACAAACAGCATCAGAAAACAGTGGGG
AATTTTGAAAAGTCATGGAGAAAAACTTGGTAGCCACGTTTCAAAGGTACACTTAGAAAATTTAATGATGAAGATTTAAT
CTCAAAACAAGACCATGAACAAGAAGCTGAAAAACTCAAATTAGAAATTCAGAAATGTAAAGAAATGATTAAAACTCAGC
AGCAACTTTTACAGCAACACCTCACTACTGCTTGTGATGATGATACCACTGCACTATTATAAGACTGTTATTTGGAAGAA
AAAGGATGCCACAAAAAATGGCCCCTTTTTAAAGAGCAAGGAGCAAAAAAATAATTTTCAGAGAGAAAGACGAAGCTTTA
CAGAAGCAGCTATTCACCTAGGTTTGGAGAGAAACATGTTT

Alignment

ORF - retro_hsap_2822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.16 %
• Parental protein coverage: 50.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RQLQCKNRNLHQLLKNEKDEVQKLQNIIASRATQYNHDMKRKEREYNKLKERLHQLVMNKKDKKIAMDIL
          RQLQCKNRNL.QLLKNEKD.VQKL.NII.S.A.QY.HDM..KE.EYNKLKE.LHQ..MN.K..KIA.DIL
Retrocopy RQLQCKNRNLNQLLKNEKDKVQKLRNIIVS*AIQYYHDMI*KECEYNKLKESLHQPFMNQKELKIALDIL

Parental  NYVGRADGKRGSWRTGKTEARN-EDEMYKILLNDYEYRQKQILMENAE-LKKVLQQMKKEMISLLSPQKK
          N.VGRADGKRG.W.TGKTE.RN..DEMYKI.LNDYEY..KQ.LMENA...KK.L.QM.K.M..LLSPQ.K
Retrocopy NNVGRADGKRGLWKTGKTEVRN<FDEMYKIILNDYEYCHKQFLMENAD>MKKFLHQMEKDMFFLLSPQ-K

Parental  KPRERVDDSTGTVISDVEEDAGELSRESMWDLSCETVREQLTNSIRKQWRILKSHVEKLDNQVSKVHLEG
          KPRER.D.STGTVISDVEEDAGE.SR.S.W.LSCETVREQ.TNSIRKQW.ILKSH.EKL...VSKVHLE.
Retrocopy KPREREDGSTGTVISDVEEDAGEMSRDSIWELSCETVREQPTNSIRKQWGILKSHGEKLGSHVSKVHLEN

Parental  -FNDEDVISRQDHEQETEKLELEIQQCKEMIKTQQQLLQQQLATAYDDDTTSLLRDCYLLEEKERLKEEW
          .FNDED.IS.QDHEQE.EKL.LEIQ.CKEMIKTQQQLLQQ.L.TA.DDDTT.LL.DCYL..E.......W
Retrocopy <FNDEDLISKQDHEQEAEKLKLEIQKCKEMIKTQQQLLQQHLTTACDDDTTALL*DCYL--EEKGCHKKW

Parental  SLFKEQ--KK-NFERERRSFTEAAIRLGLERKAF
          .LFKEQ..KK.NF.RERRSFTEAAI.LGLER..F
Retrocopy PLFKEQGAKK>NFQRERRSFTEAAIHLGLERNMF

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	3.94 RPM
bodymap2_adrenal	0.00 RPM	10.32 RPM
bodymap2_brain	0.00 RPM	138.98 RPM
bodymap2_breast	0.00 RPM	6.83 RPM
bodymap2_colon	0.00 RPM	40.78 RPM
bodymap2_heart	0.00 RPM	16.04 RPM
bodymap2_kidney	0.00 RPM	48.52 RPM
bodymap2_liver	0.00 RPM	14.11 RPM
bodymap2_lung	0.00 RPM	8.95 RPM
bodymap2_lymph_node	0.00 RPM	7.13 RPM
bodymap2_ovary	0.00 RPM	16.83 RPM
bodymap2_prostate	0.00 RPM	20.99 RPM
bodymap2_skeletal_muscle	0.00 RPM	9.29 RPM
bodymap2_testis	0.04 RPM	205.08 RPM
bodymap2_thyroid	0.00 RPM	22.15 RPM
bodymap2_white_blood_cells	0.00 RPM	22.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2822 was not detected

EST

No EST(s) were mapped for retro_hsap_2822 retrocopy.

TSS

No TSS is located nearby retro_hsap_2822 retrocopy 5' end.

Lab

retro_hsap_2822 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2822 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1913
Pongo abelii	retro_pabe_2206

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000117155	1 retrocopy	retro_hsap_2822 ,
Pongo abelii	ENSPPYG00000001201	1 retrocopy	retro_pabe_2206,
Pan troglodytes	ENSPTRG00000000906	1 retrocopy	retro_ptro_1913,
Tarsius syrichta	ENSTSYG00000004276	1 retrocopy	retro_tsyr_526,
Tursiops truncatus	ENSTTRG00000008402	1 retrocopy	retro_ttru_1078,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).