RetrogeneDB ID: retro_hsap_2463

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:25141725..25142697(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000225344
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NIPAL1
• Ensembl ID: ENSG00000163293
• Aliases: None
• Description: NIPA-like domain containing 1 [Source:HGNC Symbol;Acc:27194]

Sequence

>retro_hsap_2463
GGCTCCAGCTTCATATTGAAAAAGAAGGGTCTTTTGCAACTGGCCAACAAAAGCATCACTGGAGCTGGACAAGGTGGACA
TTCTGACCTGAAGGATGGCTCTGGGGGACAGGAGTGCTGGCCATGGGAGCAGGAGAGGCTGCACATTTTGCTGCTTATGC
TTTTGCACCTGCCATCTTGGTCACCCTCACCCCCCCGGCCCTCTGAGTGTTCTCATAAGTGCAATATTATCTTCCTATTT
TTTAAACGAGCACTTGAACATTTATGGGAAAACAGGCTGCATATTGGGGTCAACTGTGATGGTTATCCATGCCCCAGAAG
AAGAGGAAGTCACTTCTTTGCATGAAATGGAAATGAAATTGAGAGACCCAGGATTTATTTCCTTTGCTGTGATCATAATT
GTGATCTTGGTGCTGATTTTGATTGTGGCTCCCAAGAAAGGACAGACCAATATATTGGTCTATATTTCAATCTGTTCTTT
GGCTGCAGCATTTTCAATTTCTCCTGCCAAAGGCCTGGGTATTGCCATTAAGGAATTACTAGAATGGAAGCCAGTTTAGA
AGCATCCCCTGGTCATTGTTTTGCTGGCTATACTTGTGTTTTTGGTGACTACACAGATTAACTATCTCAAGGCACCAGAC
ACCGTGAATACATCTCCTGTGACTCCCATTTATTTTGCGTTCTTCACATCCATGGTAGTGACTTGCTCTGCCATCTTACT
CCAAGAGTGGTATGGCATGAAAACTGGAGATATCATCGAGACCCTGAATGGATTCTTCACTATTATCCTTGGCATCTTTC
TTCTACATGCTTTTAAAAATACTGACATTACCTGGAGTAAGCTGACATCCACTGCTAAGAAAGAAGTCATCTCTCTGAAT
GGCAATGAGAGCAGTCCTGTTTTACTAGAGAACTTGGAGTGTTCAGCCCTGGATACAATGATAACGTTACCTTGTTTAGC
AGAACTGATGAT

Alignment

ORF - retro_hsap_2463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.78 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSSFILKKKGLLQLASKGFTRAGQGGHSYLKE-WLWWVGLLSMGAGEAANFA--AYAFAPATLVTPL-GA
          GSSFILKKKGLLQLA.K..T.AGQGGHS.LK..WLW..G.L.MGAGEAA.FA..A.A.A.....TP..G.
Retrocopy GSSFILKKKGLLQLANKSITGAGQGGHSDLKD<WLWGTGVLAMGAGEAAHFAAYAFAPAILVTLTPP<GP

Parental  LSVLISAILSSYFLNEHLNIHGKIGCILSILGSTVMVIHAPQEEEVTSLHEMEMKLRDPGFISFAVIITV
          LSVLISAILSSYFLNEHLNI.GK.GC...ILGSTVMVIHAP.EEEVTSLHEMEMKLRDPGFISFAVII.V
Retrocopy LSVLISAILSSYFLNEHLNIYGKTGC---ILGSTVMVIHAPEEEEVTSLHEMEMKLRDPGFISFAVIIIV

Parental  ISLVLILIVAPKKGQTNILVYISICSLIGAFSVSSVKGLGIAIKELIEWKPVYKHPLVFVLLAVLVLSVT
          I.LVLILIVAPKKGQTNILVYISICSL..AFS.S..KGLGIAIKEL.EWKPV.KHPLV.VLLA.LV..VT
Retrocopy I-LVLILIVAPKKGQTNILVYISICSLAAAFSISPAKGLGIAIKELLEWKPV*KHPLVIVLLAILVFLVT

Parental  TQINYLNKALDTFNTSLVTPIYYVFFTSMVVTCSAILFQEWYGMTAGDIIGTLSGFFTIIIGIFLLHAFK
          TQINYL.KA.DT.NTS.VTPIY..FFTSMVVTCSAIL.QEWYGM..GDII.TL.GFFTII.GIFLLHAFK
Retrocopy TQINYL-KAPDTVNTSPVTPIYFAFFTSMVVTCSAILLQEWYGMKTGDIIETLNGFFTIILGIFLLHAFK

Parental  NTDITWSELTSTAKKEAVSLNVNENNYVLLENLECSA-PGYNDDVTLFSRTDD
          NTDITWS.LTSTAKKE..SLN.NE...VLLENLECSA.PGYND.VTLFSRTDD
Retrocopy NTDITWSKLTSTAKKEVISLNGNESSPVLLENLECSA<PGYNDNVTLFSRTDD

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	0.74 RPM
bodymap2_adrenal	0.00 RPM	0.61 RPM
bodymap2_brain	0.02 RPM	0.52 RPM
bodymap2_breast	0.00 RPM	1.73 RPM
bodymap2_colon	0.00 RPM	3.62 RPM
bodymap2_heart	0.00 RPM	0.06 RPM
bodymap2_kidney	0.00 RPM	13.13 RPM
bodymap2_liver	0.00 RPM	8.11 RPM
bodymap2_lung	0.00 RPM	0.93 RPM
bodymap2_lymph_node	0.00 RPM	0.38 RPM
bodymap2_ovary	0.00 RPM	1.75 RPM
bodymap2_prostate	0.00 RPM	10.32 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.36 RPM
bodymap2_testis	0.06 RPM	2.77 RPM
bodymap2_thyroid	0.00 RPM	8.38 RPM
bodymap2_white_blood_cells	0.00 RPM	0.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2463 was not detected

EST

No EST(s) were mapped for retro_hsap_2463 retrocopy.

TSS

No TSS is located nearby retro_hsap_2463 retrocopy 5' end.

Lab

retro_hsap_2463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2463 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1422
Gorilla gorilla	retro_ggor_1533

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002047	1 retrocopy	retro_dnov_2048,
Homo sapiens	ENSG00000163293	1 retrocopy	retro_hsap_2463 ,
Gorilla gorilla	ENSGGOG00000009006	1 retrocopy	retro_ggor_1533,
Macaca mulatta	ENSMMUG00000018625	1 retrocopy	retro_mmul_638,
Nomascus leucogenys	ENSNLEG00000017377	1 retrocopy	retro_nleu_2814,
Pongo abelii	ENSPPYG00000014714	1 retrocopy	retro_pabe_1810,
Pan troglodytes	ENSPTRG00000016038	1 retrocopy	retro_ptro_1422,

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	0.04 RPM
CEU_NA12751	0.02 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	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

---

Indel association:

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