RetrogeneDB ID: retro_nleu_1223

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397285.1:19138826..19140759(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000006867
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: XRN2
• Ensembl ID: ENSNLEG00000009991
• Aliases: None
• Description: None

Sequence

>retro_nleu_1223
CTTAATGTTCTTCGTGCGTATCTGGAAAGAGAACTCACAATGGCCAGCCTACCATTCACATTCGATGTTGAGAGGAGCAT
TGATGACTGGGTTTTCATGTGCTTCTTTGTGGGAAATGACTTCCTCCCTCATTTGCCATCGGTAGAGATTAGGGAAAATG
CAATTGACCGTTTGGTCAACATATACAAAAATGTGGCACACAAAACTGGGGTTACCTTACTGACAGTGGTTATGTCAATC
TGCAAAGAGTACAGATGATCATGTTAGCAGTTGGTGAAGTTGAGGATAGCATTTTTAAAAAGAGAAAGGATGATGAGGGC
AGTTTTAGAAGATGACAGAAAGAAAAAAGAAAGAGAATGAAGAGAGATCAACCAACCTTCACTCCTAGTGGAATATTAAC
TCCTCATGCCTTGGGTTCAAGAAATTCACCAGGTTCTCAAGTAGCCAGTAATCCGAGACAAGCAGCCTATGAAATGAGGA
TGCAGAATAACTCTAGTCCTTCAATATCTCCTAATACGAGTTTCATATCTGATGGCTCCCCATCTCTAATGGGAGGAATT
AAGCGAAAAGCAGAAGACAGTGACAGTGAACCTGAGCCAGAGGATAACGTCAGGTTATGGGAAGCTGGCTGGAAGCAGCG
GTACTACAAGAACAAATTTGACGTGGATGCAGCTGATGAGAAATTCCGTCAGAAAGTTGTGCATTCGTACGTTGAAGGAC
TTTGCTGGGTTCTTAGATATTATTATCAGGGCTGTGCTTCCTGGAAGTGGTATTATCCATTTCATTATGCGCCATTTGCT
TCAGACTTTGAAGGCATTGCAGACGTGCCATCTGATTTTGAGAAGGGTACAAAACCGTTTAAACCACTGGAACAACTTAT
GGGAGTTTTTCCAGCTGCAAGTGGTAATTTTCTTCCTCCATCATGGCGGAAGCTCATGAGTGACCCTGATTCTAGTATAA
TTGACTTCCATCCTGAAGATTTTGCTATTGATTTGAATGGGAAGAAATATGCATGGCAAGGTGTTTCTCTCTTGCCATTC
ATGGGTGAGTGAAGGCTACGAGCTGCCCTAGAAGAGGTATACCCAGACTTCACTACAGAAGAGACCAGAAGAAACAGCCT
TGGAGGTGATGTCTTATTTGTGGGGAAACATCACCCACTCCATGACTTCATTTTAGAGCTGTACCAGACAGGTTCCACAG
AGCCAGTGGATGTACCCCTGAACTATGTCATGGGATTCAAGGAAAGTTTTCTCTGGATGAAGAAGCCATTCTTCCAGATC
AAATAGTATGTTCTCCTGTTCCTATGTTAAGGGATCTGACATAGAACACTGTAGTCAGTATTAATTTTAAAGACCCACAG
TTTGCTGAAGATTATATTTTTAAAGCTGTAATGCTTCCAGGAGCAAGAAAGCTAGCAGCAGTACTGAAACCTAGTGACTG
GGAAAAATCCAGCAACGGACAGCAGTGGAAGCCTCAGCTTGGCTTTAACTGTGACCGGAGGCCTGTACACCTGGATCAGG
CAGGCTTCAGGACTTTGGGCCATGTTATGCCAAGAGGCTCAGGAACTGGCATTTACAGCAATGCTGCACCACCACCTGCG
ACTTATCAGGGAAACTTATACAGGCCGCTTTTGAGAGGACAAGCCCAGATTCCAAAACTTATGTCAAATATGAGGCCCCA
GGATTCCTGGCAAGGTCCTCCTCCCCTTTTCCAGCAGCAAAGGTTTGACGGAGGCATTGGGGCTGAACCTCTGCTCCCAT
GGAAACGGATGCTGCAAACCCAGAATGCAGCCTTCCAGCCAAACCAGTACCAGATGCTAGCTGGGCCTGGTGGGTATCCA
CCCAGACGAGATGATCTTGGAGGGAGACAGGGATATCACAGAGAAGGAAGGAAATATCCTTTGCCACCACCCTCAGGAAG
ATACAATTGAAAT

Alignment

ORF - retro_nleu_1223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.58 %
• Parental protein coverage: 67.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LNVLREYLERELTMASLPFTFDVERSIDDWVFMCFFVGNDFLPHLPSLEIRENAIDRLVNIYKNVVHKTG
          LNVLR.YLERELTMASLPFTFDVERSIDDWVFMCFFVGNDFLPHLPS.EIRENAIDRLVNIYKNV.HKTG
Retrocopy LNVLRAYLERELTMASLPFTFDVERSIDDWVFMCFFVGNDFLPHLPSVEIRENAIDRLVNIYKNVAHKTG

Parental  -GYLTESGYVNLQRVQMIMLAVGEVEDSIFKKRKDDEDSFRRRQKEKRKRMKRDQPAFTPSGILTPHALG
          .GYLT.SGYVNLQRVQMIMLAVGEVEDSIFKKRKDDE.SF..............QP.FTPSGILTPHALG
Retrocopy <GYLTDSGYVNLQRVQMIMLAVGEVEDSIFKKRKDDEGSFXXXXXXXXXXXXXXQPTFTPSGILTPHALG

Parental  SRNSPGSQVASNPRQAAYEMRMQNNSSPSISPNTSFTSDGSPSPIGGIKRKAEDSDSEPEPEDNVRLWEA
          SRNSPGSQVASNPRQAAYEMRMQNNSSPSISPNTSF.SDGSPS..GGIKRKAEDSDSEPEPEDNVRLWEA
Retrocopy SRNSPGSQVASNPRQAAYEMRMQNNSSPSISPNTSFISDGSPSLMGGIKRKAEDSDSEPEPEDNVRLWEA

Parental  GWKQRYYKNKFDVDAADEKFRRKVVQSYVEGLCWVLRYYYQGCASWKWYYPFHYAPFASDFEGIADMPSD
          GWKQRYYKNKFDVDAADEKFR.KVV.SYVEGLCWVLRYYYQGCASWKWYYPFHYAPFASDFEGIAD.PSD
Retrocopy GWKQRYYKNKFDVDAADEKFRQKVVHSYVEGLCWVLRYYYQGCASWKWYYPFHYAPFASDFEGIADVPSD

Parental  FEKGTKPFKPLEQLMGVFPAASGNFLPPSWRKLMSDPDSSIIDFYPEDFAIDLNGKKYAWQGVALLPFVD
          FEKGTKPFKPLEQLMGVFPAASGNFLPPSWRKLMSDPDSSIIDF.PEDFAIDLNGKKYAWQGV.LLPF..
Retrocopy FEKGTKPFKPLEQLMGVFPAASGNFLPPSWRKLMSDPDSSIIDFHPEDFAIDLNGKKYAWQGVSLLPFMG

Parental  ERRLRAALEEVYPDLTPEETRRNSLGGDVLFVGKHHPLHDFILELYQTGSTEPVDVP-PELCHGIQGRFS
          E.RLRAALEEVYPD.T.EETRRNSLGGDVLFVGKHHPLHDFILELYQTGSTEPVDVP.PELCHGIQG.FS
Retrocopy E*RLRAALEEVYPDFTTEETRRNSLGGDVLFVGKHHPLHDFILELYQTGSTEPVDVP<PELCHGIQGKFS

Parental  LDEEAILPDQIVCSPVPMLRDLTQNTVVSINFKDPQFAEDYIFKAVMLPGARKPAAVLKPSDWEKSSNGR
          LDEEAILPDQIVCSPVPMLRDLT.NTVVSINFKDPQFAEDYIFKAVMLPGARK.AAVLKPSDWEKSSNG.
Retrocopy LDEEAILPDQIVCSPVPMLRDLT*NTVVSINFKDPQFAEDYIFKAVMLPGARKLAAVLKPSDWEKSSNGQ

Parental  QWKPQLGFNRDRRPVHLDQAAFRTLGHVMPRGSGTGIYSNAAPPPATYQGNLYRPLLRGQAQIPKLMSNM
          QWKPQLGFN.DRRPVHLDQA.FRTLGHVMPRGSGTGIYSNAAPPPATYQGNLYRPLLRGQAQIPKLMSNM
Retrocopy QWKPQLGFNCDRRPVHLDQAGFRTLGHVMPRGSGTGIYSNAAPPPATYQGNLYRPLLRGQAQIPKLMSNM

Parental  RPQDSWRGPPPLFQQQRFDRGVGAEPLLPWNRMLQTQNAAFQPNQYQMLAGPGGYPPRRDDRGGRQGYPR
          RPQDSW.GPPPLFQQQRFD.G.GAEPLLPW.RMLQTQNAAFQPNQYQMLAGPGGYPPRRDD.GGRQGY.R
Retrocopy RPQDSWQGPPPLFQQQRFDGGIGAEPLLPWKRMLQTQNAAFQPNQYQMLAGPGGYPPRRDDLGGRQGYHR

Parental  EGRKYPLPPPSGRYNWN
          EGRKYPLPPPSGRYN.N
Retrocopy EGRKYPLPPPSGRYN*N

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_1223 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000009991	1 retrocopy	retro_nleu_1223 ,