RetrogeneDB ID: retro_hsap_545

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:17619283..17619753(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000236582
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRPF38A
• Ensembl ID: ENSG00000134748
• Aliases: None
• Description: PRP38 pre-mRNA processing factor 38 (yeast) domain containing A [Source:HGNC Symbol;Acc:25930]

Sequence

>retro_hsap_545
ATGGCTAACCGTACGGTGAAGGATGCACACAGCATCCACGGCACTAACCCTCAATATCTGGTGGAGAAGATCTTTGAACG
CGAATCTATGAGTCCAAGTTCTGGAAAGAGGAGTGCTTTGGACTTACGGCTGAACTTGCAGTCGATAAAGCCATGGAGTT
AAGGTTTGTGGGTGGCCTCTATGGTGGCAACATAAAACCAACACCCTTTCTGTGTTAAACCTTGAAGATGCTTCAAATTC
AACCCGAGAAGGATATCATTGTAGAGTTTATCAAAAATGAAGATTTCAAGTATGTCCGCATGTTGGGGGCATTTTACGTG
AGGCTAACAGGCATTGCAATTGATTGCTACAAGTACTTGGAGTCTTCCTACAATGACTATTGAAAAATCAAGAGCCAGAA
CCGAAATGAGGAGTTTGAATTGATGCATGTTGATGAGTTTGTTGATGAACTATTGCACAGTAAGAGAGTA

Alignment

ORF - retro_hsap_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 50.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANRTVKDAHSIHGTNPQYLVEKIIR-TRIYESKYWKEECFGLTAELVVDKAMELRFVGGVYGGNIKPTP
          MANRTVKDAHSIHGTNPQYLVEKI...TRIYESK.WKEECFGLTAEL.VDKAMELRFVGG.YGGNIKPTP
Retrocopy MANRTVKDAHSIHGTNPQYLVEKIFE<TRIYESKFWKEECFGLTAELAVDKAMELRFVGGLYGGNIKPTP

Parental  FLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTGTAIDCYKYLEPLYNDYRKIKSQNRNGEF
          FLC.TLKMLQIQPEKDIIVEFIKNEDFKYVRMLGA.Y.RLTG.AIDCYKYLE..YNDY.KIKSQNRN.EF
Retrocopy FLC*TLKMLQIQPEKDIIVEFIKNEDFKYVRMLGAFYVRLTGIAIDCYKYLESSYNDY*KIKSQNRNEEF

Parental  ELMHVDEFIDELLHSERV
          ELMHVDEF.DELLHS.RV
Retrocopy ELMHVDEFVDELLHSKRV

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	31.49 RPM
bodymap2_adrenal	0.00 RPM	48.66 RPM
bodymap2_brain	0.12 RPM	34.76 RPM
bodymap2_breast	0.00 RPM	34.73 RPM
bodymap2_colon	0.00 RPM	55.59 RPM
bodymap2_heart	0.00 RPM	15.19 RPM
bodymap2_kidney	0.00 RPM	47.26 RPM
bodymap2_liver	0.00 RPM	12.76 RPM
bodymap2_lung	0.00 RPM	32.86 RPM
bodymap2_lymph_node	0.00 RPM	57.51 RPM
bodymap2_ovary	0.00 RPM	117.88 RPM
bodymap2_prostate	0.00 RPM	58.70 RPM
bodymap2_skeletal_muscle	0.00 RPM	14.30 RPM
bodymap2_testis	0.00 RPM	76.20 RPM
bodymap2_thyroid	0.00 RPM	65.80 RPM
bodymap2_white_blood_cells	0.00 RPM	80.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_545 was not detected

EST

No EST(s) were mapped for retro_hsap_545 retrocopy.

TSS

No TSS is located nearby retro_hsap_545 retrocopy 5' end.

Lab

retro_hsap_545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_545 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_410

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545 ,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227, retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500, retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406, retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13, retro_tgut_14,

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	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 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	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 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	0.06 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	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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