RetrogeneDB ID: retro_hsap_411

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:78509248..78509855(-)
• Located in intron of: ENSG00000137960

Retrocopy information

• Ensembl ID: ENSG00000213561
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NIT2
• Ensembl ID: ENSG00000114021
• Aliases: None
• Description: nitrilase family, member 2 [Source:HGNC Symbol;Acc:29878]

Sequence

>retro_hsap_411
ACTTTCCACTTGGCCCTCATCCAGCTTCAAGTTTCTTCATCAAATCAGATAACAACACTCGAGCTTGTAGCCTTGTCCGG
GAGACAGCAACGCAAGGAGCCAAAATGGTTTCTTTGTTGGAATGCTTTAATTCTCCATATGGCACAAAATATTTTCCTGA
ATATGCAGCGAAAATTCCTGGTAAATCCACACAGAAGCTTTCTGAAGTAGCAAAGGAATACAACCTCACTAGAGGTTCCA
TCCCTGAAGAGGATGCTGGGAAATTAGATAACACCTATGCTGTGTTTGCACCTCATGGAACTTTACTAGTAAAGCACAGA
AAGGTCCATCTGCTTAACACTGGTGTTCCTGGAAAAATGACGTTTCAAGAATCCACAATGTTGAGTCCAGGCAACAGTTT
CTCCACATTTGATACTCCTTACTGCAGAATGAGTCGGGGCATCTGCTATGACACTGGTTTGCAGAGCTTGCACAAATCTA
CACACGGAAAGGCTGCCAGCTGTTGGTTTATCCAGGGGCTTTCAGTTTGACCACTGGACCAGCCCACTGGGAATTGCTTC
AGGCTCTTGATAATCAGGTGTATGTGGCCACATTCTCCTGCCCAAGA

Alignment

ORF - retro_hsap_411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.71 %
• Parental protein coverage: 75.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SFRLALIQLQISS-IKSDNVTRACSFIREAATQGAKIVSLPECFNSPYGAKYFPEYAEKIPGESTQKLSE
          .F.LALIQLQ.SS.IKSDN.TRACS..RE.ATQGAK.VSL.ECFNSPYG.KYFPEYA.KIPG.STQKLSE
Retrocopy TFHLALIQLQVSS<IKSDNNTRACSLVRETATQGAKMVSLLECFNSPYGTKYFPEYAAKIPGKSTQKLSE

Parental  VAKECSIYLIGGSIPEEDAGKLYNTCAVFGPDGTLLAKYRKIHLFDIDVPGKITFQESKTLSPGDSFSTF
          VAKE....L..GSIPEEDAGKL.NT.AVF.P.GTLL.K.RK.HL....VPGK.TFQES..LSPG.SFSTF
Retrocopy VAKEYN--LTRGSIPEEDAGKLDNTYAVFAPHGTLLVKHRKVHLLNTGVPGKMTFQESTMLSPGNSFSTF

Parental  DTPYCRVGLGICYDMR-FAELAQIYAQRGCQLLVYPGAFNLTTGPAHWELLQRSRAVDNQVYVATASPAR
          DTPYCR...GICYD...FAELAQIY...GCQLLVYPGAF.LTTGPAHWELLQ...A.DNQVYVAT.S..R
Retrocopy DTPYCRMSRGICYDTG<FAELAQIYTRKGCQLLVYPGAFSLTTGPAHWELLQ---ALDNQVYVATFSCPR

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	0.46 RPM	28.70 RPM
bodymap2_adrenal	0.14 RPM	15.33 RPM
bodymap2_brain	0.05 RPM	14.02 RPM
bodymap2_breast	0.47 RPM	28.95 RPM
bodymap2_colon	0.02 RPM	11.16 RPM
bodymap2_heart	0.09 RPM	20.07 RPM
bodymap2_kidney	0.12 RPM	40.02 RPM
bodymap2_liver	0.15 RPM	44.27 RPM
bodymap2_lung	0.00 RPM	16.24 RPM
bodymap2_lymph_node	0.00 RPM	13.08 RPM
bodymap2_ovary	0.23 RPM	21.22 RPM
bodymap2_prostate	0.00 RPM	22.29 RPM
bodymap2_skeletal_muscle	0.20 RPM	20.10 RPM
bodymap2_testis	0.00 RPM	14.44 RPM
bodymap2_thyroid	0.83 RPM	22.75 RPM
bodymap2_white_blood_cells	0.00 RPM	13.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_411 was not detected

EST

No EST(s) were mapped for retro_hsap_411 retrocopy.

TSS

No TSS is located nearby retro_hsap_411 retrocopy 5' end.

Lab

retro_hsap_411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_411 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_315
Gorilla gorilla	retro_ggor_406
Macaca mulatta	retro_mmul_505
Callithrix jacchus	retro_cjac_3014

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003980	1 retrocopy	retro_amel_1002,
Callithrix jacchus	ENSCJAG00000000590	1 retrocopy	retro_cjac_3014,
Homo sapiens	ENSG00000114021	1 retrocopy	retro_hsap_411 ,
Gorilla gorilla	ENSGGOG00000003724	1 retrocopy	retro_ggor_406,
Macaca mulatta	ENSMMUG00000020024	2 retrocopies	retro_mmul_1758, retro_mmul_505,
Mustela putorius furo	ENSMPUG00000011450	1 retrocopy	retro_mputfur_805,
Nomascus leucogenys	ENSNLEG00000002631	1 retrocopy	retro_nleu_1009,
Pan troglodytes	ENSPTRG00000015161	1 retrocopy	retro_ptro_315,

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	0.07 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.03 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	0.03 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	0.03 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	0.03 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	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 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).