RetrogeneDB ID: retro_hsap_994

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:49783298..49783945(+)
• Located in intron of: ENSG00000123352

Retrocopy information

• Ensembl ID: ENSG00000257954
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FGFR1OP2
• Ensembl ID: ENSG00000111790
• Aliases: FGFR1OP2, HSPC123-like, WIT3.0
• Description: FGFR1 oncogene partner 2 [Source:HGNC Symbol;Acc:23098]

Sequence

>retro_hsap_994
ATGAGTTGCACAATTGAGAAGGCACTTGCTGATGCTAAAACTCTTGTTGAAAGATTAAGAGATCACGACGATGCAGCAGA
AACTCTGATTGAGCAAACCACAGCTCTCAATAAGCGAGTAGAAGCCACGAAGCAGTATCAGAAAGAAATTCAAGAGCTTA
ATGAAGTCGCAAGAACATCGGCCACGGTCCACGTTAGTTATGGGAATCCAGCAAGAAAACAGACAAATCAGAGAATTGCA
ACAAGAAAGAAAAGAATTGCGTACATCCCTGGAAGAACATCAGTCGGCCTTGGAACTTACGATGAGCAAGTATCGAGAAC
AAATGGTTAGATTGCTAATGGCTAGCAAAAAAGATGATCCGGGAAAAATAATGAAGTTAACAAAAGCAGCACTCCAAGGA
TACAGGCACATGTTGACCAGATAAATGAAATATGGCAGCAGTAATGAAGAAAGCCATTGAAATTGACAAGCAACAGGATT
GCAAGGAACAAGAACTAATATTTCAACTTGAACAAGAAAACAAAGGCGTTAGAGAGATCCTATAAATAACTCGAGAATCA
CTTTTGAACCTAAGGAAAGAAGATGTGTCGGAAAGTACTTCTTTGTCAGCATTAGTGACCAACAGTGACTTGAGTCTGAG
GAAGAGC

Alignment

ORF - retro_hsap_994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSCTIEKALADAKALVERLRDHDDAAESLIEQTTALNKRVEAMKQYQEEIQELNEVAR-HRPRSTLVMGI
          MSCTIEKALADAK.LVERLRDHDDAAE.LIEQTTALNKRVEA.KQYQ.EIQELNEVAR.HRPRSTLVMGI
Retrocopy MSCTIEKALADAKTLVERLRDHDDAAETLIEQTTALNKRVEATKQYQKEIQELNEVAR>HRPRSTLVMGI

Parental  QQENRQIRELQQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKL-KEQHSKELQAHV
          QQENRQIRELQQE.KELRTSLEEHQSALEL.MSKYREQM.RLLMASKKDDPG.IMKL...QHSK......
Retrocopy QQENRQIRELQQERKELRTSLEEHQSALELTMSKYREQMVRLLMASKKDDPGKIMKL>QKQHSKDTGTC*

Parental  DQITEMAAVMRKAIEIDEQQGCKEQERIFQLEQENKGLREILQITRESFLNLRKDDASESTSLSALVTNS
          .....MAAVM.KAIEID.QQ.CKEQE.IFQLEQENKG.REIL.ITRES.LNLRK.D.SESTSLSALVTNS
Retrocopy PDK*NMAAVMKKAIEIDKQQDCKEQELIFQLEQENKGVREIL*ITRESLLNLRKEDVSESTSLSALVTNS

Parental  DLSLRKS
          DLSLRKS
Retrocopy DLSLRKS

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	37.15 RPM
bodymap2_adrenal	0.55 RPM	57.38 RPM
bodymap2_brain	0.02 RPM	99.71 RPM
bodymap2_breast	0.00 RPM	41.23 RPM
bodymap2_colon	0.00 RPM	49.11 RPM
bodymap2_heart	0.00 RPM	30.52 RPM
bodymap2_kidney	0.06 RPM	61.86 RPM
bodymap2_liver	0.00 RPM	15.86 RPM
bodymap2_lung	0.07 RPM	59.39 RPM
bodymap2_lymph_node	0.13 RPM	90.55 RPM
bodymap2_ovary	0.00 RPM	103.40 RPM
bodymap2_prostate	0.00 RPM	60.91 RPM
bodymap2_skeletal_muscle	0.00 RPM	26.45 RPM
bodymap2_testis	0.15 RPM	76.47 RPM
bodymap2_thyroid	0.21 RPM	48.77 RPM
bodymap2_white_blood_cells	0.00 RPM	81.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_994 was not detected

EST

No EST(s) were mapped for retro_hsap_994 retrocopy.

TSS

No TSS is located nearby retro_hsap_994 retrocopy 5' end.

Lab

retro_hsap_994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_994 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_756
Pongo abelii	retro_pabe_839

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006966	2 retrocopies	retro_dnov_2342, retro_dnov_2594,
Equus caballus	ENSECAG00000016890	1 retrocopy	retro_ecab_988,
Homo sapiens	ENSG00000111790	1 retrocopy	retro_hsap_994 ,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486,
Monodelphis domestica	ENSMODG00000016618	2 retrocopies	retro_mdom_1788, retro_mdom_244,
Mus musculus	ENSMUSG00000040242	2 retrocopies	retro_mmus_3669, retro_mmus_720,
Pongo abelii	ENSPPYG00000004375	1 retrocopy	retro_pabe_839,
Pan troglodytes	ENSPTRG00000004783	1 retrocopy	retro_ptro_756,
Tupaia belangeri	ENSTBEG00000011581	2 retrocopies	retro_tbel_3732, retro_tbel_4608,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.49 RPM
CEU_NA11843	0.68 RPM
CEU_NA11930	0.46 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.25 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.38 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.26 RPM
FIN_HG00183	0.33 RPM
FIN_HG00277	0.44 RPM
FIN_HG00315	0.28 RPM
FIN_HG00321	0.24 RPM
FIN_HG00328	0.28 RPM
FIN_HG00338	0.13 RPM
FIN_HG00349	0.43 RPM
FIN_HG00375	0.29 RPM
FIN_HG00377	0.15 RPM
FIN_HG00378	0.38 RPM
GBR_HG00099	0.29 RPM
GBR_HG00111	0.32 RPM
GBR_HG00114	0.26 RPM
GBR_HG00119	0.41 RPM
GBR_HG00131	0.95 RPM
GBR_HG00133	0.53 RPM
GBR_HG00134	0.37 RPM
GBR_HG00137	0.44 RPM
GBR_HG00142	0.42 RPM
GBR_HG00143	0.41 RPM
TSI_NA20512	0.23 RPM
TSI_NA20513	0.53 RPM
TSI_NA20518	0.25 RPM
TSI_NA20532	0.51 RPM
TSI_NA20538	0.37 RPM
TSI_NA20756	0.32 RPM
TSI_NA20765	0.66 RPM
TSI_NA20771	0.28 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.31 RPM
YRI_NA18870	0.47 RPM
YRI_NA18907	0.35 RPM
YRI_NA18916	0.42 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.16 RPM
YRI_NA19114	0.37 RPM
YRI_NA19118	0.29 RPM
YRI_NA19213	0.19 RPM
YRI_NA19214	0.17 RPM
YRI_NA19223	0.50 RPM

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Indel association:

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