RetrogeneDB ID: retro_hsap_3721

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:39873169..39874058(+)
• Located in intron of: ENSG00000237251

Retrocopy information

• Ensembl ID: ENSG00000233225
• 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_3721
ATGTTTGCCAAAGGCAGAGGCTCGGCGGTGCCCTCGGATGGGCAGGCTTGGGAAAAGTTAGCTTCATACGTCTACGAATA
TTTACTGCACGTAAGAGTACAGAAATCTGCAGAGACCTTCTTGTCGGAGATTCGATGGGAAAAAAACATCACGTTGGGAG
AACCGCCTGGGTTTTTGCACTCGTGGTGGTGTGTATTTGGGGACCTTTACTGTGCAGCTCCTCAAAGGAGAGACACTTGT
GAACATTCAAGTGAAGCAAAAGCCTTTCATGATTATAGTGCAGCAGCTGCCCCGAGCCCCGTGCTTGGCAACATTCCCCC
CAACGATGGGATGCCGGGAGGCCCCATCCCGCCAGGTTTCTTTCAGGGTCCTCCGGGGTCACAGCCCTCGCCGCACGCAC
AGCCTCCACCTCACAATCCTAGCAGCATGATGGGACCCCACAGTCAGCCTTTTATGTCACCGCGATACGTAGGCGGCCCC
GGGCCCCCGATCAGAATGGGAAACCAGCCTCCGGGAGGAGTTCTTGGGACACAGCCATTGCTGCCCAATTCTATGGATCC
CACACGACAACAAGGCCACCCCAACATGGGAGGATCAATGCAGAGAATGAACCCTCCCCGAGGCATGGGGCCCATGGGTC
CCGGCCCACAGAATTACGGCAGCGGCATGAGACCACCACCCAACTCCCTCGGCCCGCCATGCCCGGGATTAACATGGGCC
CGGGAGCTGGCAGACCCTGGCCCAATCCTAACAGTGCTAACTCAATTCCATATTCCTCCTCATCACCTGGTACCTATGTG
GGACCCCCGGTGGTGGCGGCCCTCCAGGAACACCCATTATGCCCAGTCCCGCAGATTCAACAAATTCCAGTGACAACATC
TACACAATG

Alignment

ORF - retro_hsap_3721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.65 %
• Parental protein coverage: 76.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFAKGKGSAVPSDGQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPGFLHSWWCVFWDLY
          MFAKG.GSAVPSDGQA.EKLA.YVYEYLLHV..QKSA.TFLSEIRWEKNITLGEPPGFLHSWWCVF.DLY
Retrocopy MFAKGRGSAVPSDGQAWEKLASYVYEYLLHVRVQKSAETFLSEIRWEKNITLGEPPGFLHSWWCVFGDLY

Parental  CAAPERRDTCEHSSEAKAFHDYSAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHNP
          CAAP.RRDTCEHSSEAKAFHDYSAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHNP
Retrocopy CAAPQRRDTCEHSSEAKAFHDYSAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHNP

Parental  SSMMGPHSQPFMSPRYAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGMG
          SSMMGPHSQPFMSPRY.GGP.PPIRMGNQPPGGV.GTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGMG
Retrocopy SSMMGPHSQPFMSPRYVGGPGPPIRMGNQPPGGVLGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGMG

Parental  PMGPGPQNYGSGMRPPPNSLG-PAMPGINMGPGAGRPWPNPNSANSIPYSSSSPGTYVGP-PGGGGPPGT
          PMGPGPQNYGSGMRPPPNSLG.PAMPGINMGPGAGRPWPNPNSANSIPYSSSSPGTYVGP.PGGGGPPGT
Retrocopy PMGPGPQNYGSGMRPPPNSLG<PAMPGINMGPGAGRPWPNPNSANSIPYSSSSPGTYVGP<PGGGGPPGT

Parental  PIMPSPADSTNSSDNIYTM
          PIMPSPADSTNSSDNIYTM
Retrocopy PIMPSPADSTNSSDNIYTM

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	0.60 RPM	59.08 RPM
bodymap2_adrenal	0.33 RPM	40.02 RPM
bodymap2_brain	0.66 RPM	139.16 RPM
bodymap2_breast	0.66 RPM	46.23 RPM
bodymap2_colon	0.81 RPM	85.29 RPM
bodymap2_heart	0.13 RPM	40.56 RPM
bodymap2_kidney	0.33 RPM	40.43 RPM
bodymap2_liver	0.21 RPM	20.40 RPM
bodymap2_lung	0.26 RPM	59.99 RPM
bodymap2_lymph_node	0.35 RPM	52.79 RPM
bodymap2_ovary	1.06 RPM	150.32 RPM
bodymap2_prostate	0.48 RPM	94.01 RPM
bodymap2_skeletal_muscle	0.13 RPM	38.38 RPM
bodymap2_testis	0.49 RPM	102.73 RPM
bodymap2_thyroid	0.30 RPM	34.97 RPM
bodymap2_white_blood_cells	0.51 RPM	78.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3721 was not detected

EST

No EST(s) were mapped for retro_hsap_3721 retrocopy.

TSS

No TSS is located nearby retro_hsap_3721 retrocopy 5' end.

Lab

retro_hsap_3721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3721 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	0.26 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.13 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.19 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.20 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.15 RPM
GBR_HG00111	0.13 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.10 RPM
GBR_HG00134	0.13 RPM
GBR_HG00137	0.22 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.17 RPM
TSI_NA20518	0.19 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.14 RPM
TSI_NA20786	0.08 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.17 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.13 RPM
YRI_NA19099	0.21 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.23 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.04 RPM

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Indel association:

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