RetrogeneDB ID: retro_hsap_3685

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:158658370..158659447(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000188451
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRP72
• Ensembl ID: ENSG00000174780
• Aliases: None
• Description: signal recognition particle 72kDa [Source:HGNC Symbol;Acc:11303]

Sequence

>retro_hsap_3685
CAATTTAACAAGGCATTACTTGCTATGTACACAAACCAGGCCGAACAATGCCTCAAAATATCTGCCAGTTTACATTCCCA
AAGTCCCGAGCATCTCTCACCTATGTTAACCCAAGGTGCCCAGCTCTGCGTGAAAAGCAGCACACAAAAGCAATAGAGCT
GCTTCAGGAATTTTCAGATCAGCATCAAGAAAATGCAATTGAAATTAAGCTGACCATGGCACAGTTGAAAATTTCTCAAG
AGAATATTTCTTAGCATGTCTAATATTGAGAAGCAGAGAGGAGTTAAAGCAGAAACCAGGCATGGTGTCTGCATTAGTGA
CCATGTGTAGCCATGAAGAAGATTTAATAGTACCACTGATGTCTTCACACAAGCTATCTGGTGGTATCAAAACCATCAGC
TCAAATCTCCTGCTCATTTGTCCTTGATAAAAGAAGCTGCAAACTTCAAGCTCAAATATGGGCGGGAGGAGGCAATTAGT
GACCTAGAACAGCTATGGAAACAAAATCCAAAAGATATTCATACCCTGGCACAGTTTATTTCTGCTTACTCACTTGCAGA
TCCAGAGAAAGGCACAGCTCTTAGTAAACATTTGCCATCATCAGATAGTATGTCTCTAAAAGTAGATGTTGAGGCTCTTG
AAAATTCTCCTGGTGCTACATACATTTGGAAGGGTGGAAAAGTTACTAGAGATAGTCAACCAAAGGAACAAGGAAAGGGA
GATTTGAAAAAGAAAAAGAAGGGAAAATTGCCTAAGAATTATGACCCAAAACTTACCCCAGATCCAGAAAGATGGCTGCC
AATGCAAGAATGTTCTTTCTACCAGGGAAGAAAGAAGGGTAAAAAGAAGGATCAGATGGGAAAAGGGACCCAGGGAGCAA
CTGCAGGAGCTTCATCTGAACTGGATGCCAGAAAAACTGTGAGTAGCCCACCCACCTCCCCAAGACCTGGCAGTGCAGCG
ACACTATCTGCCTCTACAAGTAACATCATACCCCCAAGACACCAGAGACCTGCAGGGGCTCCAGCAACAAAAAAGAAACA
GCAACAGAAAAAGAAGAAAGGTGGAAAAGGTGGCTGG

Alignment

ORF - retro_hsap_3685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 59.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EFNKALLAMYTNQAEQCRKISASLQSQSPEHLLPVLIQAAQLC-REKQHTKAIELLQEFSDQHPENAAEI
          .FNKALLAMYTNQAEQC.KISASL.SQSPEHL.P.L.Q.AQLC.REKQHTKAIELLQEFSDQH.ENA.EI
Retrocopy QFNKALLAMYTNQAEQCLKISASLHSQSPEHLSPMLTQGAQLC<REKQHTKAIELLQEFSDQHQENAIEI

Parental  KLTMAQLKISQGNIS-KACLILRSIEELKHKPGMVSALVTMYSHEEDI-DSAIEVFTQAIQWYQNHQPKS
          KLTMAQLKISQ.NIS..ACLILRS.EELK.KPGMVSALVTM.SHEED...S...VFTQAI.WYQNHQ.KS
Retrocopy KLTMAQLKISQENIS<LACLILRSREELKQKPGMVSALVTMCSHEEDL<NSTTDVFTQAIWWYQNHQLKS

Parental  PAHLSLIREAANFKLKYGRKKEAISDLQQLWKQNPKDIHTLAQLISAYSLVDPEKAKALSKHLPSSDSMS
          PAHLSLI.EAANFKLKYGR..EAISDL.QLWKQNPKDIHTLAQ.ISAYSL.DPEK..ALSKHLPSSDSMS
Retrocopy PAHLSLIKEAANFKLKYGRE-EAISDLEQLWKQNPKDIHTLAQFISAYSLADPEKGTALSKHLPSSDSMS

Parental  LKVDVEALENSAGATYIRKKGGKVTGDSQPKEQGQGDLKKKKKKKKGKLPKNYDPKVTPDPERWLPMRER
          LKVDVEALENS.GATYI.K.GGKVT.DSQPKEQG.GDL...KKKKKGKLPKNYDPK.TPDPERWLPM.E.
Retrocopy LKVDVEALENSPGATYIWK-GGKVTRDSQPKEQGKGDL---KKKKKGKLPKNYDPKLTPDPERWLPMQEC

Parental  SYYRGRKKGKKKDQIGKGTQGATAGASSELDASKTVSSPPTSPRPGSAATVSASTSNIIPPRHQKPAGAP
          S.Y.GRKKGKKKDQ.GKGTQGATAGASSELDA.KTVSSPPTSPRPGSAAT.SASTSNIIPPRHQ.PAGAP
Retrocopy SFYQGRKKGKKKDQMGKGTQGATAGASSELDARKTVSSPPTSPRPGSAATLSASTSNIIPPRHQRPAGAP

Parental  ATKKKQQQKKKKGGKGGW
          A...............GW
Retrocopy AXXXXXXXXXXXXXXXGW

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	0.04 RPM	92.81 RPM
bodymap2_adrenal	0.23 RPM	97.88 RPM
bodymap2_brain	0.09 RPM	95.21 RPM
bodymap2_breast	0.02 RPM	75.70 RPM
bodymap2_colon	0.00 RPM	81.54 RPM
bodymap2_heart	0.09 RPM	41.76 RPM
bodymap2_kidney	0.21 RPM	97.09 RPM
bodymap2_liver	0.04 RPM	73.59 RPM
bodymap2_lung	0.00 RPM	103.29 RPM
bodymap2_lymph_node	0.00 RPM	79.27 RPM
bodymap2_ovary	0.08 RPM	131.08 RPM
bodymap2_prostate	0.00 RPM	104.44 RPM
bodymap2_skeletal_muscle	0.02 RPM	44.41 RPM
bodymap2_testis	0.11 RPM	101.01 RPM
bodymap2_thyroid	0.00 RPM	121.76 RPM
bodymap2_white_blood_cells	0.00 RPM	126.08 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3685 was not detected

EST

No EST(s) were mapped for retro_hsap_3685 retrocopy.

TSS

No TSS is located nearby retro_hsap_3685 retrocopy 5' end.

Lab

retro_hsap_3685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3685 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017998	1 retrocopy	retro_cjac_2538,
Homo sapiens	ENSG00000174780	2 retrocopies	retro_hsap_1939, retro_hsap_3685 ,
Nomascus leucogenys	ENSNLEG00000008806	1 retrocopy	retro_nleu_2909,
Oryctolagus cuniculus	ENSOCUG00000012226	1 retrocopy	retro_ocun_989,
Rattus norvegicus	ENSRNOG00000002100	1 retrocopy	retro_rnor_587,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.14 RPM
FIN_HG00277	0.22 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.09 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.06 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.19 RPM
GBR_HG00131	0.23 RPM
GBR_HG00133	0.17 RPM
GBR_HG00134	0.15 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.12 RPM
TSI_NA20518	0.14 RPM
TSI_NA20532	0.20 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.19 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.12 RPM
YRI_NA19213	0.12 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.10 RPM

---

Indel association:

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