RetrogeneDB ID: retro_hsap_513

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:221723129..221723864(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000227585
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC35E3
• Ensembl ID: ENSG00000175782
• Aliases: None
• Description: solute carrier family 35, member E3 [Source:HGNC Symbol;Acc:20864]

Sequence

>retro_hsap_513
TTATATTTGCCTCAACATGTCTGCCACCCCAAGATCCTCCTTCTGGCCTTTAGCTTCTGTGATTACAAGGTCTTCACCAA
CTTCTCTCTGCAGGGCAACTCCACAGGCGTCCATCAGCTGATCAAGGTCATCATTACACTGGTGATTATGGCCATGCAGA
CCCTCTGCTACCAGAAGGCCTTCTTCACCAGAATATAACACAACACTGATTCCTGTAACTTTAGGTGTAATCCTAAATTC
TTATTACAATGTGAAATGTAATGTCCTTGGAAGGATGTTTTCTGCTCTCAGTGTTTTAGTTATACCCCCTTATCCAGTGT
GGGCAGAAACCAAGCAGAATGAGTTTCAAGTAAACTCAATGCTGCTGCAGCACTATCAAGCACCAATACCTTCTGCTGTT
ATTGGTTGCTTCTCTGAGTCAGTGCATGGAGAGCAAGAAATATCTAGTCTCTGGTCAGCTTCTGCTTTGCCTATGGTGCA
GCTATCTGAAATAATGGTTGTCATGGTGAACTTATCAATTCACTGGGTCACTAGGTACACTTCATCAGTCACCTATGACA
TGTTTGGGCACTTCAAGTTCTGACTTGCTTTATTTGGAGGACATGTGTTATTTAAAGATCCACTGTTAATTAACCAGAGT
CTTGGCATTTTATGTAGTTATTTGGTGTAAGAATAAGAGCTTATATTCATTCTGTACTCTATAAACAGGAAGGAAGAAAA
TGTAAATTGCTACAA

Alignment

ORF - retro_hsap_513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58. %
• Parental protein coverage: 78.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IFAPKSLPPSRLLLLALSFCGFVVFTNLSLQNNTIGTYQLAKAMTTPVIIAIQTFCYQKTFSTRI-QLTL
          ...P........LLLA.SFC...VFTN.SLQ.N..G..QL.K...T.VI.A.QT.CYQK.F.TRI...TL
Retrocopy LYLPQHVCHPKILLLAFSFCDYKVFTNFSLQGNSTGVHQLIKVIITLVIMAMQTLCYQKAFFTRI>NTTL

Parental  IPITLGVILNSYYDVKFNFLGMVFAALGVLVTSLYQVWVGAKQHELQVNSMQLLYYQAPMSSAMLLVAVP
          IP.TLGVILNSYY.VK.N.LG..F.AL.VLV...Y.VW...KQ.E.QVNSM.L..YQAP..SA...V...
Retrocopy IPVTLGVILNSYYNVKCNVLGRMFSALSVLVIPPYPVWAETKQNEFQVNSMLLQHYQAPIPSA---VIGC

Parental  FFEPVFGEGGIFGPWSVSALLMVLLSGVIAFMVNLSIYWIIGNTSPVTYNMFGHFKFCITLFGGYVLFKD
          F.E.V.GE..I...WS.SAL.MV.LS.....MVNLSI.W....TS.VTY.MFGHFKF...LFGG.VLFKD
Retrocopy FSESVHGEQEISSLWSASALPMVQLSEIMVVMVNLSIHWVTRYTSSVTYDMFGHFKF*LALFGGHVLFKD

Parental  PLSINQALGILCT-LFG--ILAYTHFKLSEQEGSRSKLAQ
          PL.INQ.LGILC..LFG..I.AY.H..L..QEG...KL.Q
Retrocopy PLLINQSLGILCS<LFGVRIRAYIHSVLYKQEGRKCKLLQ

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	14.81 RPM
bodymap2_adrenal	0.00 RPM	17.05 RPM
bodymap2_brain	0.00 RPM	16.95 RPM
bodymap2_breast	0.00 RPM	12.67 RPM
bodymap2_colon	0.00 RPM	6.67 RPM
bodymap2_heart	0.00 RPM	6.39 RPM
bodymap2_kidney	0.00 RPM	12.00 RPM
bodymap2_liver	0.00 RPM	7.22 RPM
bodymap2_lung	0.00 RPM	5.73 RPM
bodymap2_lymph_node	0.00 RPM	9.76 RPM
bodymap2_ovary	0.00 RPM	10.64 RPM
bodymap2_prostate	0.00 RPM	13.06 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.49 RPM
bodymap2_testis	0.40 RPM	8.77 RPM
bodymap2_thyroid	0.00 RPM	14.22 RPM
bodymap2_white_blood_cells	0.00 RPM	13.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_513 was not detected

EST

No EST(s) were mapped for retro_hsap_513 retrocopy.

TSS

No TSS is located nearby retro_hsap_513 retrocopy 5' end.

Lab

retro_hsap_513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_513 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_383
Gorilla gorilla	retro_ggor_473
Bos taurus	retro_btau_642

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031919	1 retrocopy	retro_btau_642,
Choloepus hoffmanni	ENSCHOG00000013347	1 retrocopy	retro_chof_2348,
Cavia porcellus	ENSCPOG00000004322	3 retrocopies	retro_cpor_1404, retro_cpor_1487, retro_cpor_339,
Homo sapiens	ENSG00000175782	1 retrocopy	retro_hsap_513 ,
Gorilla gorilla	ENSGGOG00000012605	1 retrocopy	retro_ggor_473,
Mus musculus	ENSMUSG00000060181	1 retrocopy	retro_mmus_287,
Pan troglodytes	ENSPTRG00000005201	1 retrocopy	retro_ptro_383,
Pteropus vampyrus	ENSPVAG00000002545	1 retrocopy	retro_pvam_710,

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	0.00 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	0.00 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	0.00 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

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Indel association:

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