RetrogeneDB ID: retro_nleu_1542

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397298.1:5251022..5251556(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000002832
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPATCH11
• Ensembl ID: ENSNLEG00000027017
• Aliases: None
• Description: G patch domain containing 11 [Source:HGNC Symbol;Acc:26768]

Sequence

>retro_nleu_1542
ATGAAGTTGAACATGGCAGAAGAAGAGGACTAACATCTGATTCCTTCATCAATGTCCAAGAAGATATCAGACCAGGCTTG
TCAATGCTAAGGCAAATCCGGGAAGCCCGTGGAAAAGAAGAAAAGCAACAGGAAGCTAATTTGAAACACAGGCAGAAGAG
TTTAAAAGAAGAACAAAAAAGACGTGACATTGGGTTGAAGAATTCACTAGGCTGTGAAAACAAAGGGTTTGCCTTGCTCC
AAAAGATGGGTTATAAAAGTGGTCAGGCACTTGGCACGAGTGGGGGTGGTATTGTTAAACCGATTCCTCTCAATATCAAA
AAAGGGAAAAGTGGCATTTGGTCATGAGGCATCATTAAAACAGAAAGCAGAGGAAAAATTAGAAAGCTACAGAAAAAAGA
TTCACATGAATAACCAAGCTGAAGAAAAAGCTGCAGACCAGTTTCGAATGTGACTTAAAAATAAGCAAGATGAAATGAAG
CTAGGAGATCTCAGAAGAAGCCAGCGAGTCTGTCAACAATTGGACACCCAGAAA

Alignment

ORF - retro_nleu_1542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.01 %
• Parental protein coverage: 90.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKLNMAEEED-YMSDSFINVQEDIRPGLPMLRQIREARRKEEKQQEANLKNRQKSLKEEEQERRDIGLKN
          MKLNMAEEED...SDSFINVQEDIRPGL.MLRQIREAR.KEEKQQEANLK.RQKSLKEE.Q.RRDIGLKN
Retrocopy MKLNMAEEED<LTSDSFINVQEDIRPGLSMLRQIREARGKEEKQQEANLKHRQKSLKEE-QKRRDIGLKN

Parental  ALGCENKGFALLQKMGYKSGQALGKSGGGIVEPIPLNIKTGKSGI-GHEASLKRKAEEKLESYRKKIHMK
          .LGCENKGFALLQKMGYKSGQALG.SGGGIV.PIPLNIK.GKSGI.GHEASLK.KAEEKLESYRKKIHM.
Retrocopy SLGCENKGFALLQKMGYKSGQALGTSGGGIVKPIPLNIKKGKSGI>GHEASLKQKAEEKLESYRKKIHMN

Parental  NQAEEKAAEQFRMRLKNKQDEMKLEGDLRRSQRACQQLDAQK
          NQAEEKAA.QFRM.LKNKQDEMKL.GDLRRSQR.CQQLD.QK
Retrocopy NQAEEKAADQFRM*LKNKQDEMKL-GDLRRSQRVCQQLDTQK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1542 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006041	1 retrocopy	retro_cfam_708,
Choloepus hoffmanni	ENSCHOG00000004377	3 retrocopies	retro_chof_1420, retro_chof_2292, retro_chof_398,
Homo sapiens	ENSG00000152133	1 retrocopy	retro_hsap_2802,
Monodelphis domestica	ENSMODG00000015289	1 retrocopy	retro_mdom_1855,
Nomascus leucogenys	ENSNLEG00000027017	1 retrocopy	retro_nleu_1542 ,
Pan troglodytes	ENSPTRG00000011832	1 retrocopy	retro_ptro_1899,