RetrogeneDB ID: retro_hsap_2887

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:178977538..178979061(-)
• Located in intron of: ENSG00000171121

Retrocopy information

• Ensembl ID: ENSG00000240429
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LRRFIP1
• Ensembl ID: ENSG00000124831
• Aliases: LRRFIP1, FLAP-1, FLAP1, FLIIAP1, GCF-2, GCF2, HUFI-1, TRIP
• Description: leucine rich repeat (in FLII) interacting protein 1 [Source:HGNC Symbol;Acc:6702]

Sequence

>retro_hsap_2887
TTGACCAGCCCCGCGGCCACGCAGAGCCGGGAGATCTACTGTTTGAGCGCGGAAGCGCAGAGGCTGGCGGAGGCCCGGCT
CGCCGCAAAACGGGAGGCCCGCGCGGAGGCTCGTGAGATCCCCATGAAGGAGCTGGAGCGGCAGCAGAAGGAGGTAGAAG
AGAGACCAGAAAAATATTTTACTGAGAAGGGGTCTCGTAACATGCTGGGCCCGTCTGCAGCCACGCTGGCCTTTCTGGGT
GGGACTTCCTCTCAGAGAGGCAGCGGAGACACCTCTATATCCATCGACACCGAGGCGTCCATCAGGGAAATCAAGGACTC
TCTAGCAGAAGTTGAAGAGAAATGTAAGAAGGCTATGTTTTCCAATGCTCAGTTAGACAATGAAAACACAAACTTCATTT
ACCAAGTTGACACCCTGAAAGATATGTTGCTGGAGATTGAAGAACAGCTGGCTGAATATAGGCGGCAGTACGAAGAGAAA
AACAAATAATTTGAAAGGGAAAAACACGCCCACAGTATACTGCAGTTTCAGTTTGCTGAAGTCAAGGAGGCCCTGAAGCA
AACAGAGGAAATGCTCGAGAAACATGGAATAATCCTAAATTCAGAAATAGTTACCAATGGAGAGACTTCCGACACTCTCA
GTAATGTTTGATACCAAGATCCTACCAAGATGACGAAAGAAGAGTTAAATGCCCTCAAGTCGACAGGGGATGGGACCCTA
GGAAAGCCAGTGAGGTGGAGGTGAAGAATGAAATCGTGGCGAATGTGGGGAAAAGAGAAATCTTGCACAATACTGAGAAA
GAACAACACACAGAGGACACAGTGAAGGATTGTGTGGACATAGAGGTATTCACTGCTGGTGAGAATACCGAGGACCAGAA
ATCCTCTGAAGACACTGCCCCATTCCTAGGAACCTTAGCAGGTGCTACCTATGAGGAACAGGTTCAAAGCCAAATTCTTG
AGAGCGCTTCTCTCCCTGAAAACACAGCACAGGTTGAGTCAAATGAGGTCATGGGTGCACCAGATGACAGGACCAGAACT
CCCCTTGAGCCATCCAACTGTTGGAGTGACTTAGATGGTGGGAGCCACACAGAGAATGTGGGAGAGGCAGCGGTGACTCA
GGTTGGAGAGCAGGCAGACACAGTGGCCTCATGTCCTTTAGGGCATAGTGATGACACAGTTTATCATGATGACAGATGTA
TGGTAGAGGTCCCCCAACAGTTAGAGACAAGCATAGGGCATAGTTTAGAGAAAGAATTCACCAACCAGGAAGCAGCTGAG
CCCAAGGAGGTTCCAGTGCAGAGTACAGAAGCAGGTAGGGATCACAACGAAGAAGAGGGTGAAGAAAAAGGATTAAGGGA
TGAGAAACCAATCAAGACAGAAGTTCCTGGTTCTCCAGCAGGAACTGAGAGCAAGGGTCAGGAGGCGACAGGTCCAAGTA
CAGTAGACACTCAAAGTGAACCCTCAGATATGAAAGAGCCAGATGAAGAAAAGAATGACCAACAGGGAGAGGCATTGGAC
TCA

Alignment

ORF - retro_hsap_2887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.16 %
• Parental protein coverage: 67.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTSPAAAQSREIDCLSPEAQKLAEARLAAKRAARAEAREIRMKELERQQKEVEERPEKDFTEKGSRNMPG
          .TSPAA.QSREI.CLS.EAQ.LAEARLAAKR.ARAEAREI.MKELERQQKEVEERPEK.FTEKGSRNM.G
Retrocopy LTSPAATQSREIYCLSAEAQRLAEARLAAKREARAEAREIPMKELERQQKEVEERPEKYFTEKGSRNMLG

Parental  LSAATLASLGGTSSRRGSGDTSISIDTEASIREIKDSLAEVEEKYKKAMVSNAQLDNEKTNFMYQVDTLK
          .SAATLA.LGGTSS.RGSGDTSISIDTEASIREIKDSLAEVEEK.KKAM.SNAQLDNE.TNF.YQVDTLK
Retrocopy PSAATLAFLGGTSSQRGSGDTSISIDTEASIREIKDSLAEVEEKCKKAMFSNAQLDNENTNFIYQVDTLK

Parental  DMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVKEALKQREEMLEKHGIILNSEIATNGETS
          DMLLE.EEQLAE.RRQYEEKNK.FEREKHAHSILQFQFAEVKEALKQ.EEMLEKHGIILNSEI.TNGETS
Retrocopy DMLLEIEEQLAEYRRQYEEKNK*FEREKHAHSILQFQFAEVKEALKQTEEMLEKHGIILNSEIVTNGETS

Parental  DTLNNVGYQGPTKMTKEELNALKSTGDGTLGR-ASEVEVKNEIVANVGKREILHNTEKEQHTEDTVKDCV
          DTL.NV.YQ.PTKMTKEELNALKSTGDGTLG..ASEVEVKNEIVANVGKREILHNTEKEQHTEDTVKDCV
Retrocopy DTLSNV*YQDPTKMTKEELNALKSTGDGTLGK<ASEVEVKNEIVANVGKREILHNTEKEQHTEDTVKDCV

Parental  DIEVFPAGENTEDQKSSEDTAPFLGTLAGATYEEQVQSQILESSSLPENTVQVESNEVMGAPDDRTRTPL
          DIEVF.AGENTEDQKSSEDTAPFLGTLAGATYEEQVQSQILES.SLPENT.QVESNEVMGAPDDRTRTPL
Retrocopy DIEVFTAGENTEDQKSSEDTAPFLGTLAGATYEEQVQSQILESASLPENTAQVESNEVMGAPDDRTRTPL

Parental  EPSNCWSDLDGGNHTENVGEAAVTQVEEQAGTVASCPLGHSDDTVYHDDKCMVEVPQELETSTGHSLEKE
          EPSNCWSDLDGG.HTENVGEAAVTQV.EQA.TVASCPLGHSDDTVYHDD.CMVEVPQ.LETS.GHSLEKE
Retrocopy EPSNCWSDLDGGSHTENVGEAAVTQVGEQADTVASCPLGHSDDTVYHDDRCMVEVPQQLETSIGHSLEKE

Parental  FTNQEAAEPKEVPAHSTEVGRDHNEEEGEETGLRDEKPIKTEVPGSPAGTEGNCQEATGPSTVDTQNEPL
          FTNQEAAEPKEVP..STE.GRDHNEEEGEE.GLRDEKPIKTEVPGSPAGTE...QEATGPSTVDTQ.EP.
Retrocopy FTNQEAAEPKEVPVQSTEAGRDHNEEEGEEKGLRDEKPIKTEVPGSPAGTESKGQEATGPSTVDTQSEPS

Parental  DMKEPDEEKSDQQGEALDS
          DMKEPDEEK.DQQGEALDS
Retrocopy DMKEPDEEKNDQQGEALDS

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	0.44 RPM	132.51 RPM
bodymap2_adrenal	1.51 RPM	161.54 RPM
bodymap2_brain	0.80 RPM	58.98 RPM
bodymap2_breast	0.45 RPM	106.42 RPM
bodymap2_colon	1.01 RPM	255.16 RPM
bodymap2_heart	0.39 RPM	115.53 RPM
bodymap2_kidney	0.74 RPM	191.46 RPM
bodymap2_liver	0.38 RPM	57.44 RPM
bodymap2_lung	0.12 RPM	205.85 RPM
bodymap2_lymph_node	1.61 RPM	133.87 RPM
bodymap2_ovary	0.67 RPM	97.39 RPM
bodymap2_prostate	1.35 RPM	244.72 RPM
bodymap2_skeletal_muscle	0.55 RPM	95.05 RPM
bodymap2_testis	1.51 RPM	80.48 RPM
bodymap2_thyroid	1.22 RPM	143.72 RPM
bodymap2_white_blood_cells	0.18 RPM	428.76 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_2887 in 31 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	3:178979022..178979365
ENCFF002CFX	POLR2A	3:178979023..178979349
ENCFF002CGN	POLR2A	3:178979039..178979340
ENCFF002CHO	POLR2A	3:178978909..178979402
ENCFF002CIO	POLR2A	3:178979039..178979260
ENCFF002CJZ	POLR2A	3:178979085..178979301
ENCFF002CKX	POLR2A	3:178979027..178979299
ENCFF002CLM	POLR2A	3:178978935..178979475
ENCFF002CMI	POLR2A	3:178978864..178979410
ENCFF002COJ	POLR2A	3:178979010..178979446
ENCFF002CQC	POLR2A	3:178979024..178979321
ENCFF002CQE	POLR2A	3:178979126..178979339
ENCFF002CQG	POLR2A	3:178978945..178979469
ENCFF002CQI	POLR2A	3:178979091..178979231
ENCFF002CQK	POLR2A	3:178979007..178979326
ENCFF002CQM	POLR2A	3:178979030..178979307
ENCFF002CQO	POLR2A	3:178979040..178979296
ENCFF002CSY	POLR2A	3:178979013..178979313
ENCFF002CUP	POLR2A	3:178979026..178979342
ENCFF002CXM	POLR2A	3:178978945..178979435
ENCFF002CXO	POLR2A	3:178978980..178979404
ENCFF002CXP	POLR2A	3:178979145..178979273
ENCFF002CXR	POLR2A	3:178979075..178979297
ENCFF002DAH	POLR2A	3:178979040..178979324
ENCFF002DBB	POLR2A	3:178979056..178979256
ENCFF002DBE	POLR2A	3:178979104..178979285
ENCFF002DBO	POLR2A	3:178979059..178979301
ENCFF002DBP	POLR2A	3:178979061..178979286
ENCFF002DBQ	POLR2A	3:178979011..178979381
ENCFF002DBT	POLR2A	3:178978998..178979368
ENCFF002CZW	POLR2A	3:178978730..178979480

EST

2 EST(s) were mapped to retro_hsap_2887 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BE166271	178977783	178978103	95.3	304	9	290
DB281879	178977998	178978549	98.8	547	4	542

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_131962	931 libraries	697 libraries	191 libraries	6 libraries	4 libraries
TSS #2	TSS_131963	1128 libraries	611 libraries	86 libraries	2 libraries	2 libraries

The graphical summary, for retro_hsap_2887 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_2887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2887 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2001
Macaca mulatta	retro_mmul_1455

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000124831	1 retrocopy	retro_hsap_2887 ,
Gorilla gorilla	ENSGGOG00000008411	1 retrocopy	retro_ggor_2001,
Macaca mulatta	ENSMMUG00000003386	1 retrocopy	retro_mmul_1455,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.31 RPM
CEU_NA11843	0.43 RPM
CEU_NA11930	1.14 RPM
CEU_NA12004	0.91 RPM
CEU_NA12400	0.56 RPM
CEU_NA12751	2.96 RPM
CEU_NA12760	1.12 RPM
CEU_NA12827	0.99 RPM
CEU_NA12872	0.76 RPM
CEU_NA12873	0.45 RPM
FIN_HG00183	1.73 RPM
FIN_HG00277	1.59 RPM
FIN_HG00315	1.08 RPM
FIN_HG00321	2.30 RPM
FIN_HG00328	1.37 RPM
FIN_HG00338	1.28 RPM
FIN_HG00349	1.31 RPM
FIN_HG00375	1.22 RPM
FIN_HG00377	1.26 RPM
FIN_HG00378	2.23 RPM
GBR_HG00099	1.63 RPM
GBR_HG00111	1.35 RPM
GBR_HG00114	1.42 RPM
GBR_HG00119	2.01 RPM
GBR_HG00131	2.13 RPM
GBR_HG00133	1.95 RPM
GBR_HG00134	1.55 RPM
GBR_HG00137	1.32 RPM
GBR_HG00142	1.92 RPM
GBR_HG00143	1.40 RPM
TSI_NA20512	0.59 RPM
TSI_NA20513	2.35 RPM
TSI_NA20518	1.64 RPM
TSI_NA20532	2.07 RPM
TSI_NA20538	2.76 RPM
TSI_NA20756	1.37 RPM
TSI_NA20765	1.76 RPM
TSI_NA20771	1.42 RPM
TSI_NA20786	0.99 RPM
TSI_NA20798	1.84 RPM
YRI_NA18870	1.90 RPM
YRI_NA18907	2.29 RPM
YRI_NA18916	1.87 RPM
YRI_NA19093	0.89 RPM
YRI_NA19099	1.17 RPM
YRI_NA19114	1.00 RPM
YRI_NA19118	2.05 RPM
YRI_NA19213	1.89 RPM
YRI_NA19214	2.04 RPM
YRI_NA19223	3.18 RPM

---

Indel association:

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