RetrogeneDB ID: retro_pabe_411

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:88054608..88055289(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD3
• Ensembl ID: ENSPPYG00000025827
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 3 [Source:HGNC Symbol;Acc:21906]

Sequence

>retro_pabe_411
ATGGGTGGGACCACCAGCACCCGCCGGGTCACCTTCGAGGTGGACGAGAATGAGAACACCACCGTGGTGAAGGGCATCCA
GCTTTCGGAAAATGTGATTGATGGAATGAAGGAATCCTCTCCATCTGGTTCGAAGTCTCAGCGGTATTCTGGTGCTTATG
GTGCCTCAGTTTCTGATGAAGAATTGAAAAGAAGAGTAGCTGAGGAGCTGGCATTGGAGCAAGCCAAGAAAGAATCTGAA
GATCAGAAACGACTAAAGCAAGCCAAAGAGCTGGACCGAGAGAGGGCTGCTGCCAATGAGCAGTTAACCAGAGCCATCCT
TCGGGAGGGGATATCTAGCGAGGAGGAACGCGCTAAGGCAAAGCACCTGGCTAGGCAGCTAGAAGAGAAAGACCGAGTGC
TAAAGAAGCAGGATGCATTCTACAAAGAATAGCTGGCTAGACTGGAGGAGAGGAGCTCAGAATTCTACAGAGTCACCACT
GAACAATATCAGAAAGCTGCTGAAGAGGTGGAAGCAAAGTTCAAGCGGTATGAGTCTCACCCAGTCTGTGCTGATCTGCA
GGCCAAAATTCTTCAGCGTTGCCGTGAGAACACCCACCAGACCCTCAAATGCTCCACTCTGGCCACCCAGTATATGCACT
GTGTCAATCATGTCCAACAGAGCATGCTTGAGAAGGGAGGA

Alignment

ORF - retro_pabe_411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGGTTSTRRVTFEADENENITVVKGIRLSENVIDRMKESSPSGSKSQRYSGAYGASVSDEELKRRVAEEL
          MGGTTSTRRVTFE.DENEN.TVVKGI.LSENVID.MKESSPSGSKSQRYSGAYGASVSDEELKRRVAEEL
Retrocopy MGGTTSTRRVTFEVDENENTTVVKGIQLSENVIDGMKESSPSGSKSQRYSGAYGASVSDEELKRRVAEEL

Parental  ALEQAKKESEDQKRLKQAKELDRERAAANEQLTRAILRERISSEEERAKAKHLARQLEEKDRVLKKQDAF
          ALEQAKKESEDQKRLKQAKELDRERAAANEQLTRAILRE.ISSEEERAKAKHLARQLEEKDRVLKKQDAF
Retrocopy ALEQAKKESEDQKRLKQAKELDRERAAANEQLTRAILREGISSEEERAKAKHLARQLEEKDRVLKKQDAF

Parental  YKEQLARLEERSSEFYRVTTEQYQKAAEEVEAKFKRYESHPVCADLQARILQCYRENTHQTLKCSALATQ
          YKE.LARLEERSSEFYRVTTEQYQKAAEEVEAKFKRYESHPVCADLQA.ILQ..RENTHQTLKCS.LATQ
Retrocopy YKE*LARLEERSSEFYRVTTEQYQKAAEEVEAKFKRYESHPVCADLQAKILQRCRENTHQTLKCSTLATQ

Parental  YMHCVNHAKQSMLEKGG
          YMHCVNH..QSMLEKGG
Retrocopy YMHCVNHVQQSMLEKGG

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	10.56 RPM
SRP007412_cerebellum	0.00 RPM	6.93 RPM
SRP007412_heart	0.06 RPM	26.28 RPM
SRP007412_kidney	0.03 RPM	13.13 RPM
SRP007412_liver	0.03 RPM	8.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_411 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_411 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001312	1 retrocopy	retro_cfam_374,
Dasypus novemcinctus	ENSDNOG00000004942	1 retrocopy	retro_dnov_2559,
Homo sapiens	ENSG00000106554	3 retrocopies	retro_hsap_358, retro_hsap_3759, retro_hsap_542,
Macaca mulatta	ENSMMUG00000001671	1 retrocopy	retro_mmul_14,
Mus musculus	ENSMUSG00000053768	1 retrocopy	retro_mmus_3452,
Nomascus leucogenys	ENSNLEG00000012967	3 retrocopies	retro_nleu_168, retro_nleu_716, retro_nleu_904,
Oryctolagus cuniculus	ENSOCUG00000014032	1 retrocopy	retro_ocun_801,
Pongo abelii	ENSPPYG00000025827	5 retrocopies	retro_pabe_2492, retro_pabe_3161, retro_pabe_345, retro_pabe_411 , retro_pabe_501,
Pan troglodytes	ENSPTRG00000019711	4 retrocopies	retro_ptro_2550, retro_ptro_282, retro_ptro_407, retro_ptro_701,
Rattus norvegicus	ENSRNOG00000013211	1 retrocopy	retro_rnor_2874,
Sorex araneus	ENSSARG00000012111	1 retrocopy	retro_sara_592,
Ictidomys tridecemlineatus	ENSSTOG00000022282	1 retrocopy	retro_itri_1301,