RetrogeneDB ID: retro_hsap_755

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:18210546..18211170(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000255138
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GLTP
• Ensembl ID: ENSG00000139433
• Aliases: None
• Description: glycolipid transfer protein [Source:HGNC Symbol;Acc:24867]

Sequence

>retro_hsap_755
ATGGCTCTGCTGACCGAACACCTGCTGAAGCCGCTGCCCGCGGACAAGCAGATCGAGACTGGGCCCTTCCTCGAGGCGGT
GTCCCACCTGCCGCCCTTCTTCGATTGCCTTGGGTCCCCAGTGTTTACTCCCATCAAGGCAGACATAAGCAGCAACATCA
CAAAAATCAAAGCTGTGTACGACACCAACCCAGCCAAGTTCCGGACCCTGCAGAACATCCTGGAGGTGGAGAAAGAAATG
TATGGAGCAGAGCGGCTCAAAGTAGGGGCCACGCTGGCGCTGATGTGGCTGAAAAGAGGCCTCCGCTTCATCCAGGTCTT
CCTCCAGAGCATCTGCAACGAGGAGCCGGACGAGAACCACCTCAACCTCATCCGCGTCAACGCCACCAAGGCCTACGAAA
TGGCCCTCATGAAGTACCACGGCTGGATCGTGCAGATCTTCCAGGCAGCACTGTACGCAGCCTCCTGTAAGTCCGACTTC
CTGAAAGCGCTCTCCAAGGGGCAGAATGTGACGGAGGAGGAGTGCCTGGAAAAGATCCGCCTCTTCCTAGTCAACTACAT
GGCGACCATCGATGTCATCTACGAGACGTATACCCAGATGAACGCTGAGCTTAACTACAAGGTG

Alignment

ORF - retro_hsap_755 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALLAEHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTNPAKFRTL
          MALL.EHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADIS.NITKIKAVYDTNPAKFRTL
Retrocopy MALLTEHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISSNITKIKAVYDTNPAKFRTL

Parental  QNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQVFLQSICDGERDENHPNLIRVNATKAYEMALKKYH
          QNILEVEKEMYGAE..KVGATLALMWLKRGLRFIQVFLQSIC..E.DENH.NLIRVNATKAYEMAL.KYH
Retrocopy QNILEVEKEMYGAERLKVGATLALMWLKRGLRFIQVFLQSICNEEPDENHLNLIRVNATKAYEMALMKYH

Parental  GWIVQKIFQAALYAAPYKSDFLKALSKGQNVTEEECLEKIRLFLVNYTATIDVIYEMYTQMNAELNYKV
          GWIVQ.IFQAALYAA..KSDFLKALSKGQNVTEEECLEKIRLFLVNY.ATIDVIYE.YTQMNAELNYKV
Retrocopy GWIVQ-IFQAALYAASCKSDFLKALSKGQNVTEEECLEKIRLFLVNYMATIDVIYETYTQMNAELNYKV

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	54.82 RPM
bodymap2_adrenal	0.02 RPM	37.07 RPM
bodymap2_brain	0.00 RPM	36.10 RPM
bodymap2_breast	0.02 RPM	32.92 RPM
bodymap2_colon	0.00 RPM	34.28 RPM
bodymap2_heart	0.00 RPM	19.57 RPM
bodymap2_kidney	0.00 RPM	50.01 RPM
bodymap2_liver	0.00 RPM	11.87 RPM
bodymap2_lung	0.00 RPM	47.31 RPM
bodymap2_lymph_node	0.00 RPM	34.12 RPM
bodymap2_ovary	0.02 RPM	33.81 RPM
bodymap2_prostate	0.02 RPM	48.08 RPM
bodymap2_skeletal_muscle	0.00 RPM	20.68 RPM
bodymap2_testis	0.00 RPM	27.53 RPM
bodymap2_thyroid	0.00 RPM	42.95 RPM
bodymap2_white_blood_cells	0.00 RPM	69.01 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_755 was not detected

EST

No EST(s) were mapped for retro_hsap_755 retrocopy.

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_12422	1501 libraries	291 libraries	37 libraries	0 libraries	0 libraries
TSS #2	TSS_12423	762 libraries	811 libraries	248 libraries	7 libraries	1 library

The graphical summary, for retro_hsap_755 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_755 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_755 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_41
Pongo abelii	retro_pabe_28

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034092	1 retrocopy	retro_cjac_1284,
Homo sapiens	ENSG00000106086	1 retrocopy	retro_hsap_1110,
Homo sapiens	ENSG00000116095	1 retrocopy	retro_hsap_2060,
Homo sapiens	ENSG00000139433	1 retrocopy	retro_hsap_755 ,
Myotis lucifugus	ENSMLUG00000012545	5 retrocopies	retro_mluc_1056, retro_mluc_1902, retro_mluc_2135, retro_mluc_2397, retro_mluc_658,
Macaca mulatta	ENSMMUG00000022761	1 retrocopy	retro_mmul_2261,
Pongo abelii	ENSPPYG00000004939	1 retrocopy	retro_pabe_28,
Pan troglodytes	ENSPTRG00000005431	1 retrocopy	retro_ptro_41,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 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	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.04 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).