RetrogeneDB ID: retro_hsap_2155

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:130750813..130751610(+)
• Located in intron of: ENSG00000180178

Retrocopy information

• Ensembl ID: ENSG00000217289
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSBP3
• Ensembl ID: ENSG00000157216
• Aliases: SSBP3, CSDP, SSDP, SSDP1
• Description: single stranded DNA binding protein 3 [Source:HGNC Symbol;Acc:15674]

Sequence

>retro_hsap_2155
CAGGGTCCTCCGGGGTCACAGCCCTCGCCGCACGCACAGCCTCCACCTCACAATCCTAGCAGCATGATGGGACCCCACAG
TCAGCCTTTCATGTCACCGCGATACGCAGGCGGCCCCAGGCCCCCCGATCAGAATGGGAAACCAGCCTCCGGGAGGAGTT
CCTGGGACACAGCCATTGCTGCCCAATTCCATGGATCCCGCACGACAACAAGGCCATCCCCACATGGGAGGATCAATGCA
GAGAATGAACCCTCCCCGAGGCATGGGGCCCACGGGTCCCAGCCCACAGAATTACGGCAGCGGCATGAGACCACCACGCA
ATTCCCTCGGCCCCCCATGCCCGGGATTAACATGGGCCCGGGAGCCGGCAGACCCTGGCCCAATCCTAACAGTGCTAACT
CAATTCCATACTCCTCCTCATCACCTGGTACCTATGTGGGACCCCCTGGTGGTGGCGGCCCTCCAGGAACACCCACTATG
CCCAGTCCCTCAGATTCAACAAATTCCAGCGACATCTACACAATGATTAATCCGGTGCCGCCTGGAGGCAGCCGGTCCAA
CTTCCCGATGGGTCCCGGCTCGGACGGTCGGATGGGCAGCATGGGCGGCATGGAGCCACACCACATGAACGGATTGTTAG
GGTCAGGCGACATAGATGGCTTCCAAAAAATTCTCCTAACAACGTAAATAGTATTAGCAATCCTCCAGGCACCCCTCGAG
ATGACGGAGAGTTAGGAGGGAACTTCCTCCACTCCTTTCAGAATGACAATTATTCTCCAAGCATGACGATGAGTGTG

Alignment

ORF - retro_hsap_2155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 68.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QGPPGSQPSPHAQPPPHNPSSMMGPHSQPFMSPRYAGGPR-PPIRMGNQPPGGVPGTQPLLPNSMDPTRQ
          QGPPGSQPSPHAQPPPHNPSSMMGPHSQPFMSPRYAGGPR.PPIRMGNQPPGGVPGTQPLLPNSMDP.RQ
Retrocopy QGPPGSQPSPHAQPPPHNPSSMMGPHSQPFMSPRYAGGPR>PPIRMGNQPPGGVPGTQPLLPNSMDPARQ

Parental  QGHPNMGGSMQRMNPPRGMGPMGPGPQNYGSGMRPPPNSLG-PAMPGINMGPGAGRPWPNPNSANSIPYS
          QGHP.MGGSMQRMNPPRGMGP.GP.PQNYGSGMRPP.NSLG.P.MPGINMGPGAGRPWPNPNSANSIPYS
Retrocopy QGHPHMGGSMQRMNPPRGMGPTGPSPQNYGSGMRPPRNSLG<PPMPGINMGPGAGRPWPNPNSANSIPYS

Parental  SSSPGTYVGPPGGGGPPGTPIMPSPADSTNSSDNIYTMINPVPPGGSRSNFPMGPGSDGPMGGMGGMEPH
          SSSPGTYVGPPGGGGPPGTP.MPSP.DSTNSSD.IYTMINPVPPGGSRSNFPMGPGSDG.MG.MGGMEPH
Retrocopy SSSPGTYVGPPGGGGPPGTPTMPSPSDSTNSSD-IYTMINPVPPGGSRSNFPMGPGSDGRMGSMGGMEPH

Parental  HMNGSLGSGDIDG-LPKNSPNNISGISNPPGTPRDDGELGGNFLHSFQNDNYSPSMTMSV
          HMNG.LGSGDIDG.LPKNSPNN...ISNPPGTPRDDGELGGNFLHSFQNDNYSPSMTMSV
Retrocopy HMNGLLGSGDIDG<LPKNSPNNVNSISNPPGTPRDDGELGGNFLHSFQNDNYSPSMTMSV

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	0.02 RPM	59.08 RPM
bodymap2_adrenal	0.00 RPM	40.02 RPM
bodymap2_brain	0.00 RPM	139.16 RPM
bodymap2_breast	0.02 RPM	46.23 RPM
bodymap2_colon	0.02 RPM	85.29 RPM
bodymap2_heart	0.00 RPM	40.56 RPM
bodymap2_kidney	0.06 RPM	40.43 RPM
bodymap2_liver	0.02 RPM	20.40 RPM
bodymap2_lung	0.25 RPM	59.99 RPM
bodymap2_lymph_node	0.07 RPM	52.79 RPM
bodymap2_ovary	0.04 RPM	150.32 RPM
bodymap2_prostate	0.07 RPM	94.01 RPM
bodymap2_skeletal_muscle	0.00 RPM	38.38 RPM
bodymap2_testis	0.00 RPM	102.73 RPM
bodymap2_thyroid	0.00 RPM	34.97 RPM
bodymap2_white_blood_cells	0.20 RPM	78.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2155 was not detected

EST

2 EST(s) were mapped to retro_hsap_2155 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EC452556	130750893	130750999	100	101	0	97
EC524572	130750893	130750999	100	102	0	99

TSS

No TSS is located nearby retro_hsap_2155 retrocopy 5' end.

Lab

retro_hsap_2155 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2155 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005029	1 retrocopy	retro_cjac_3827,
Homo sapiens	ENSG00000130511	1 retrocopy	retro_hsap_1911,
Homo sapiens	ENSG00000145687	1 retrocopy	retro_hsap_3622,
Homo sapiens	ENSG00000157216	6 retrocopies	retro_hsap_1302, retro_hsap_1384, retro_hsap_2155 , retro_hsap_2319, retro_hsap_2539, retro_hsap_3721,
Macropus eugenii	ENSMEUG00000009291	1 retrocopy	retro_meug_1372,
Oryctolagus cuniculus	ENSOCUG00000005903	1 retrocopy	retro_ocun_252,
Pan troglodytes	ENSPTRG00000000770	2 retrocopies	retro_ptro_2618, retro_ptro_2931,

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	0.02 RPM
CEU_NA12760	0.04 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	0.06 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	0.03 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.05 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).