RetrogeneDB ID: retro_hsap_3920

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:150209649..150210881(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213205
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STRADB
• Ensembl ID: ENSG00000082146
• Aliases: STRADB, ALS2CR2, CALS-21, ILPIP, ILPIPA, PAPK
• Description: STE20-related kinase adaptor beta [Source:HGNC Symbol;Acc:13205]

Sequence

>retro_hsap_3920
AGTTCAAGAACACAAGTTGAATCACTCAAACATGAAAAACAAGTCTGAAACCAGTATCCATCAATACTTGGTCGAAGAGC
CAACCCTTTCCTGGTCGCCTCCATCCACTAGAGCCAGTGAAGTAGTATGTTCCGCCAACGTTTCTCACTACGAGCTCCAA
GTAGAAATAGGAAGAGGATTTGACAAGTTGACTTCTGTCCATCTAGCACGGCATACTCCTACGGGAACGCTGGTAACTAC
AAAAATTACAAATCTGGAAAACGGCAATAAAGAACGCCTGAAAGTTTTACAGAAAGCCATGATTCTATCCCACTTTTTCC
GGCATCCCAATATTACAACTTATTGGACAGTTTTCACTGTTGGCAGCTGGCTTTGGGTTATTTCTCCATTTATGGCCTAT
GGTTCAGCAAGACAACTCTTGAGGACCTATTTTCCTGAAGGAATGAGTAAAACTTTAATAAGAAACATTCTCTTTGGAGC
AGTGAGAGGATTGAACTATCTCTACCAATATGGCTGTATTCACAGGAGAATTAAAGCCAGCCATATCCTCATTTCTGGTG
ATGGCCTAGTGACCCTCTCTGGCCTGTCCCATCTGCATAGTTTGGTTAAGCATGGACAGAGGCATAGGGCTGTGTATGAT
TTCCCACAGTTCAGCACATTAGTGCAGCCATGGCTGAGTCCAGAACTACTGAGACAGGATTTACATGGGTATAATGTGAA
GTCAGATATTTACAGTGTTGGGATTACAACATGTGAATTAGCCAGTGGGCAGGTGCCTTTCCAGGACGTGCATAGAACTC
AGATGCTGTTAACAGAAACTGAAAGGTCCCCCTTATAGCCCATTGGATATCAGTATTTTCCCTCAATCAGAATCCAAAAT
GAAAAATTCCCGGTCAGGTGTAGACTCTGGGATTGGAGCAAGTGTGCTTGTCTCCAGTGGAACTCACACAGTAAATAGTG
ACCGATTACACACACCATCCTCAAAAACCTTCTCTCCTGCCTTCTTTAGCTGGGTACAGCTGTGTTTGCAACAAGATCCG
GAGAAAAGGCCATCAGCAAGCAGTTTATTGTCCCATGTTTTCTTCAAACAGATGAAAGAAGAAAGCCAGGATTCGGTACT
TTCACTGTTGCCTCCTGCTTATAACAAGCCATCAATATCACTGCCTCCGGTGTTACCTTGGACTGAGCCAGAATGTGGTT
TTCCTGATGAAAAAGATTCATATTGGGAATTC

Alignment

ORF - retro_hsap_3920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.96 %
• Parental protein coverage: 98.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TSRTQVESLRPEKQ-SETSIHQYLVDEPTLSWSRPSTRASEVLCSTNVSHYELQVEIGRGFDNLTSVHLA
          .SRTQVESL..EKQ.SETSIHQYLV.EPTLSWS.PSTRASEV.CS.NVSHYELQVEIGRGFD.LTSVHLA
Retrocopy SSRTQVESLKHEKQ>SETSIHQYLVEEPTLSWSPPSTRASEVVCSANVSHYELQVEIGRGFDKLTSVHLA

Parental  RHTPTGTLVTIKITNLENCNEERLKALQKAVILSHFFRHPNITTYWTVFTVGSWLWVISPFMAYGSASQL
          RHTPTGTLVT.KITNLEN.N.ERLK.LQKA.ILSHFFRHPNITTYWTVFTVGSWLWVISPFMAYGSA.QL
Retrocopy RHTPTGTLVTTKITNLENGNKERLKVLQKAMILSHFFRHPNITTYWTVFTVGSWLWVISPFMAYGSARQL

Parental  LRTYFPEGMSETLIRNILFGAVRGLNYLHQNGCIHRSIKASHILISGDGLVTLSGLSHLHSLVKHGQRHR
          LRTYFPEGMS.TLIRNILFGAVRGLNYL.Q.GCIHR.IKASHILISGDGLVTLSGLSHLHSLVKHGQRHR
Retrocopy LRTYFPEGMSKTLIRNILFGAVRGLNYLYQYGCIHRRIKASHILISGDGLVTLSGLSHLHSLVKHGQRHR

Parental  AVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGITACELASGQVPFQDMHRTQMLL-QKLKGPPY
          AVYDFPQFST.VQPWLSPELLRQDLHGYNVKSDIYSVGIT.CELASGQVPFQD.HRTQMLL.QKLKGPPY
Retrocopy AVYDFPQFSTLVQPWLSPELLRQDLHGYNVKSDIYSVGITTCELASGQVPFQDVHRTQMLL>QKLKGPPY

Parental  SPLDISIFPQSESRMKNSQSGVDSGIGESVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLVQLCLQQDPEK
          SPLDISIFPQSES.MKNS.SGVDSGIG.SVLVSSGTHTVNSDRLHTPSSKTFSPAFFS.VQLCLQQDPEK
Retrocopy SPLDISIFPQSESKMKNSRSGVDSGIGASVLVSSGTHTVNSDRLHTPSSKTFSPAFFSWVQLCLQQDPEK

Parental  RPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDEKDSYWEF
          RPSASSLLSHVFFKQMKEESQDS.LSLLPPAYNKPSISLPPVLPWTEPEC.FPDEKDSYWEF
Retrocopy RPSASSLLSHVFFKQMKEESQDSVLSLLPPAYNKPSISLPPVLPWTEPECGFPDEKDSYWEF

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	24.77 RPM
bodymap2_adrenal	0.14 RPM	11.16 RPM
bodymap2_brain	0.00 RPM	24.99 RPM
bodymap2_breast	0.00 RPM	41.81 RPM
bodymap2_colon	0.00 RPM	11.68 RPM
bodymap2_heart	0.00 RPM	58.47 RPM
bodymap2_kidney	0.02 RPM	37.76 RPM
bodymap2_liver	0.00 RPM	46.94 RPM
bodymap2_lung	0.00 RPM	26.81 RPM
bodymap2_lymph_node	0.00 RPM	18.09 RPM
bodymap2_ovary	0.00 RPM	13.96 RPM
bodymap2_prostate	0.00 RPM	13.87 RPM
bodymap2_skeletal_muscle	0.02 RPM	48.87 RPM
bodymap2_testis	0.17 RPM	22.34 RPM
bodymap2_thyroid	0.00 RPM	18.19 RPM
bodymap2_white_blood_cells	0.00 RPM	15.49 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_3920 in 5 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CHO	POLR2A	7:150211821..150212367
ENCFF002CIH	POLR2A	7:150211827..150212331
ENCFF002CIO	POLR2A	7:150211779..150212323
ENCFF002CQA	POLR2A	7:150211728..150212298
ENCFF002CQG	POLR2A	7:150211854..150212378

EST

No EST(s) were mapped for retro_hsap_3920 retrocopy.

TSS

No TSS is located nearby retro_hsap_3920 retrocopy 5' end.

Lab

retro_hsap_3920 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3920 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2638
Pongo abelii	retro_pabe_3192
Macaca mulatta	retro_mmul_1741

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000082146	2 retrocopies	retro_hsap_147, retro_hsap_3920 ,
Gorilla gorilla	ENSGGOG00000012183	1 retrocopy	retro_ggor_2638,
Macaca mulatta	ENSMMUG00000018141	1 retrocopy	retro_mmul_1741,
Nomascus leucogenys	ENSNLEG00000006967	1 retrocopy	retro_nleu_2158,
Otolemur garnettii	ENSOGAG00000010744	1 retrocopy	retro_ogar_1019,
Pongo abelii	ENSPPYG00000013074	1 retrocopy	retro_pabe_3192,

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	0.07 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 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	0.03 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

---

Indel association:

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