RetrogeneDB ID: retro_pabe_3143

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:57414901..57415368(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NHP2
• Ensembl ID: ENSPPYG00000016105
• Aliases: None
• Description: H/ACA ribonucleoprotein complex subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5RC65]

Sequence

>retro_pabe_3143
ATGACCAAAATAAAGGTAGATTCGACGGGCCCGAGGCTCAGGAGGAGGCGTGCGCCGGGGAGCCCACCTACCAGGAGCTG
CTGGTTAACCAGAACCCCATCACGCAGCCCCTGGCTTCTTGCCGCCTCACGCGGAACCTCTACAAATGCATCAAGAAAGC
CATGAAGCAGAAGCAGCTTCGGCGCGGGGTGAAAGAGGTTCAGAAATTTGTCAACAAAGGAGAAAAAGGGATCATGGTTT
TTCAGGAGACACACTGCCCACTGAGGTATACTGCCATCTTCCAGTCATGTGTGAGGACCGAAATCTGGNCCTAATGTCTC
TNATCCCTTCTAAGACGGACCTGGGGTGCAGCCCGCAGGCTCCAAGCGCNCCCACCTTGTGTNGATAATGGTCAAGCCCA
CACGAGGAGTACCAAGGAGGCCTACGACCAAAGTGCCTGGGAGGAGGTGCAGTCCCTACCCCTACCC

Alignment

ORF - retro_pabe_3143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.84 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTKIKADP-DGPEAQAEACSGERTYQELLVNQNPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQK
          MTKIK.D..DGPEAQ.EAC.GE.TYQELLVNQNPI.QPLAS.RLTR.LYKCIKKA.KQKQ.RRGVKEVQK
Retrocopy MTKIKVDS<DGPEAQEEACAGEPTYQELLVNQNPITQPLASCRLTRNLYKCIKKAMKQKQLRRGVKEVQK

Parental  FVNKGEKGIMV-LAGDTLPIEVYCHLPVMCEDRNLPYV-YIPSKTDLGAA--AGSKRPTCVIMVKPHDEY
          FVNKGEKGIMV...GDTLP.EVYCHLPVMCEDRNL.....IPSKTDLG....A.S....C.....PH.EY
Retrocopy FVNKGEKGIMV<FSGDTLPTEVYCHLPVMCEDRNLXLMSXIPSKTDLGCSPQAPSXPTLCX*WSSPHEEY

Parental  Q-EAYDE-CLEEVQSLPLP
          Q.EAYD....EEVQSLPLP
Retrocopy Q>EAYDQSAWEEVQSLPLP

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.20 RPM
SRP007412_cerebellum	0.00 RPM	3.77 RPM
SRP007412_heart	0.00 RPM	1.66 RPM
SRP007412_kidney	0.03 RPM	4.74 RPM
SRP007412_liver	0.00 RPM	3.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3143 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3143 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1702

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012244	1 retrocopy	retro_cjac_264,
Homo sapiens	ENSG00000145912	2 retrocopies	retro_hsap_3712, retro_hsap_611,
Gorilla gorilla	ENSGGOG00000000015	1 retrocopy	retro_ggor_2509,
Macropus eugenii	ENSMEUG00000003839	2 retrocopies	retro_meug_285, retro_meug_320,
Macaca mulatta	ENSMMUG00000018757	1 retrocopy	retro_mmul_1702,
Monodelphis domestica	ENSMODG00000004231	1 retrocopy	retro_mdom_345,
Mus musculus	ENSMUSG00000001056	1 retrocopy	retro_mmus_565,
Oryctolagus cuniculus	ENSOCUG00000016057	1 retrocopy	retro_ocun_151,
Ochotona princeps	ENSOPRG00000007907	3 retrocopies	retro_opri_305, retro_opri_421, retro_opri_810,
Pongo abelii	ENSPPYG00000016105	3 retrocopies	retro_pabe_1704, retro_pabe_3143 , retro_pabe_481,
Rattus norvegicus	ENSRNOG00000004247	2 retrocopies	retro_rnor_1436, retro_rnor_2198,
Sus scrofa	ENSSSCG00000014032	1 retrocopy	retro_sscr_407,