RetrogeneDB ID: retro_nleu_1786

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397308.1:9626993..9628474(-)
• Located in intron of: ENSNLEG00000003621

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD2
• Ensembl ID: ENSNLEG00000006305
• Aliases: None
• Description: None

Sequence

>retro_nleu_1786
ATGGAGGAGGGAGGATGGGACAAGACGCTGGCGCAGTCCCGGCGGCCCCCAGCGGCAGCTCCCAGCGGCACGGCCGAGAA
GCCGAGCAGCAAGGAGCAGTGGGATGCCGGGCACAAGGACAAAGAACAGGAGCTGTCTGAGGAAGATAAACAGCTTCAAG
ATGAACTGGAGACGCTCGTGGAACGACTCAGGGAGAAGTACACATCCCTGTATTGATCAGCGCTGGAGGAATTGTGAAGG
CAGATTTGTTCTTCTACAACTTCCATGACTTCAGTGCCCAAGCCTCTCAAATTTCTGCGTCCACACTATGGCCAGCTGAA
GGAAATCTATGAGAACATGGCCTCTGGGGAGAATAAGCGTTTTGCTGTGACATCATCTCTGTTTTGGCCACGACCATGAG
TGGGGAATGCGAGTGCCTCAAGTATTGGCTAGTAGGCTCCCAGAAGGAATTGGCATCTTGGGGTCATGAGTATGTCAGGC
ATCTGGCAGGAGAAGTGGCTAAGGAGTGGCAGGAGCTAGATGATGTGGAGATGGTCCAGCAGGAGCCACTGCTCACTCTG
GTGAAGGAAATCGTCCCCTACAACATGGCCCACAACACAGAGCATGAGGCCTGTGACCTGCTTATGGAAAGTGAGCAGGC
GGACCTGCTGGAGAAGGACATTGATGAGAATGCATACACCAAGGGCTGCCTTTATCTCACCAGTTGTGTGAATTATGTGT
CTGAGCCTGAGAACTCAGTCCTACTGTGTTGTGCCCTGGGTGTGTTCTGAAAGTTTAGCCGCTTCCCTGAAGCTCTGTGA
TTGGCATTGATGCTCAATGACATGGAGCTGGTAAAAGACATCTTCACATCCTGCAAGGATGTGGTAGTACAGAAACAGAT
GGCATTCATGCTAGGCTGGCATGGGGTGTTCCTGGAGCTGAGTGAAGATGTCGAGGAGTATGAGCACCTGACAGAGATAA
TGTCCAATGTACAGCTCAACAGCAACTTCTTGGCCTTAGCTCGGGAGCTGGACATCATGGAGCCCAAGGTGCCTGACGAC
ACCCACAAAACCCACCTAGAGAACAACAGGTTTGCAGGCAGTGGCTCTCAGGTGGACTCTGCCCGCATGAACCTGGCCTC
CTCTTTTGTGAATGGCTTTGTGAATGCAGCTTTTGGCCAAGACAAGCTGCTAACAGATGATGGCAACAAATGGCTTTACA
AGAACAAGGACCATGGAATGTTGAGTGCAGCTGCATCTCTTGGGATGCTGCTGCTGTGGGATGTGGATGGTGGCCTCATG
CAGATTGACAAGTACCTGTACTCCCTCTGAGGACTACATGAAGTCAGGAGTTCTTGCCTGTGGCATAGTGAACTCTGGAG
TCCGGAATGAGTGTGTCCCTGCTCTGGGACTGCTTTCAGACTATGTTCTCCACAACAGCAACACCATGAGACTTGGTTCC
ATCTTTGGGCTAGGCTTGACCTATGCTGGCTCAATCGTGAG

Alignment

ORF - retro_nleu_1786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.15 %
• Parental protein coverage: 54.52 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEEGGRDKAPVQPQQSLAAAPGGTDEKPSSKERRDAGDKDKEQELSEEDKQLQDELEMLVERLGEKDTSL
          MEEGG.DK...Q.....AAAP.GT.EKPSSKE..DAG.KDKEQELSEEDKQLQDELE.LVERL.EK.TSL
Retrocopy MEEGGWDKTLAQSRRPPAAAPSGTAEKPSSKEQWDAGHKDKEQELSEEDKQLQDELETLVERLREKYTSL

Parental  YRPALEELRRQIRSSTTSMTSVPKPLKFLRPHYGKLKEIYENMAPGENKRFAA-DIISVLAMTMSGEREC
          Y..ALEEL.RQI.SSTTSMTSVPKPLKFLRPHYG.LKEIYENMA.GENKRFA..DIISVLA.TMSGE.EC
Retrocopy Y*SALEEL*RQICSSTTSMTSVPKPLKFLRPHYGQLKEIYENMASGENKRFAV<DIISVLATTMSGECEC

Parental  LKYRLVGSQEELASWGHEYVRHLAGEVAKEWQELDDAEKVQREPLLTLVKEIVPYNMAHNAEHEACDLLM
          LKY.LVGSQ.ELASWGHEYVRHLAGEVAKEWQELDD.E.VQ.EPLLTLVKEIVPYNMAHN.EHEACDLLM
Retrocopy LKYWLVGSQKELASWGHEYVRHLAGEVAKEWQELDDVEMVQQEPLLTLVKEIVPYNMAHNTEHEACDLLM

Parental  EIEQVDMLEKDIDENAYAKVCLYLTSCVNYVPEPENSALLRCALGVFRKFSRFPEALRLALMLNDMELVE
          E.EQ.D.LEKDIDENAY.K.CLYLTSCVNYV.EPENS.LL.CALGVF.KFSRFPEAL.LALMLNDMELV.
Retrocopy ESEQADLLEKDIDENAYTKGCLYLTSCVNYVSEPENSVLLCCALGVF*KFSRFPEAL*LALMLNDMELVK

Parental  DIFTSCKDVVVQKQMAFMLGRHGVFLELSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPKVPDDIY
          DIFTSCKDVVVQKQMAFMLG.HGVFLELSEDVEEYE.LTEIMSNVQLNSNFLALARELDIMEPKVPDD..
Retrocopy DIFTSCKDVVVQKQMAFMLGWHGVFLELSEDVEEYEHLTEIMSNVQLNSNFLALARELDIMEPKVPDDTH

Parental  KTHLENNRFGGSGSQVDSARMNLASSFVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILL
          KTHLENNRF.GSGSQVDSARMNLASSFVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGM.LL
Retrocopy KTHLENNRFAGSGSQVDSARMNLASSFVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMLLL

Parental  WDVDGGLTQIDKYLYS-SEDYIKSGALLACGIVNSGVRNECDPALALLSDYVLHNSNTMRLGSIFGLGLA
          WDVDGGL.QIDKYLYS.SEDY.KSG..LACGIVNSGVRNEC.PAL.LLSDYVLHNSNTMRLGSIFGLGL.
Retrocopy WDVDGGLMQIDKYLYS>SEDYMKSG-VLACGIVNSGVRNECVPALGLLSDYVLHNSNTMRLGSIFGLGLT

Parental  YAGS-NRE
          YAGS.NRE
Retrocopy YAGS<NRE

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_1786 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000175166	1 retrocopy	retro_hsap_531,
Gorilla gorilla	ENSGGOG00000027136	1 retrocopy	retro_ggor_486,
Mus musculus	ENSMUSG00000006998	2 retrocopies	retro_mmus_209, retro_mmus_3247,
Nomascus leucogenys	ENSNLEG00000006305	1 retrocopy	retro_nleu_1786 ,
Pongo abelii	ENSPPYG00000014354	1 retrocopy	retro_pabe_218,
Pan troglodytes	ENSPTRG00000015689	1 retrocopy	retro_ptro_397,