RetrogeneDB ID: retro_nleu_2975

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397539.1:81064..81801(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PANK3
• Ensembl ID: ENSNLEG00000004896
• Aliases: None
• Description: None

Sequence

>retro_nleu_2975
ATGAAGATCAAAGATGCCAAGAAACCCTCTCTCTCATGGTTTGGCATGGACATTGAGAGAACTCTAGTAAAACTCTCGTA
CTTTGAACCTATTGCTATCACAGCAGAGGAAGAACAAGAAGAAGTTGAGAGTTTAAAAAGTATTCGAAAATATTTGATTT
CTAATGTAGCATATGGATCCACCGGCATTAGGGATGTACACCTTGAACTGAAAGATTTAACACTTTTTGGTCGAAGAGGG
AACTTGCACTTTATCAGGTTTCCAACCCAGGACCTGCCTACTTTTATCCAAATGGGAAGAGATAAAAGCTTCTCAAGATT
GCAAACGGTGCTATGTGCTACAGGAGGTGGTGCCTACAAGTTTGAAAAAGATTTTCGCGCCATTGGAAACCTCCACCTGC
ACAAACTGGATGAACTTGACTGCCTTGTAAAGGGCTTGCTGTATATAGACTGTTGGTTTCAATGGACATGCGGAGTGTTA
TTGTTTAGCTAATGCCACAGAACCTCAGCAATGCCAAAAGATTCCTTTTAACCTGGATGATCCCTACCCACTGCTTGTAG
TGAACACTGGCTCAGGAGTCAGTATTTTAGCAGTCCATTCCAAAGACATCTATAAACGAATGACTGGGACAAGCCTTGGG
GAGGGTACCTTTCTGGGTTTATGTAGTTTATTGACTGGCTGTAAGAGTTTTGAAGAGGCTCTTGAAATGGCATTCCAAAG
GTGACAGCACACAAGCT

Alignment

ORF - retro_nleu_2975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.35 %
• Parental protein coverage: 66.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKIKDAKKPSFPWFGMDIGGTLVKLSYFEPIDITAEEEQEEVESLKSIRKYLTSNVAYGSTGIRDVHLEL
          MKIKDAKKPS..WFGMDI..TLVKLSYFEPI.ITAEEEQEEVESLKSIRKYL.SNVAYGSTGIRDVHLEL
Retrocopy MKIKDAKKPSLSWFGMDIERTLVKLSYFEPIAITAEEEQEEVESLKSIRKYLISNVAYGSTGIRDVHLEL

Parental  KDLTLFGRRGNLHFIRFPTQDLPTFIQMGRDKNFSTLQTVLCATGGGAYKFEKDFRTIGNLHLHKLDELD
          KDLTLFGRRGNLHFIRFPTQDLPTFIQMGRDK.FS.LQTVLCATGGGAYKFEKDFR.IGNLHLHKLDELD
Retrocopy KDLTLFGRRGNLHFIRFPTQDLPTFIQMGRDKSFSRLQTVLCATGGGAYKFEKDFRAIGNLHLHKLDELD

Parental  CLV-KGLLY-IDSVSFNGQAECYYFANASEPERCQKMPFNLDDPYPLLVVNIGSGVSILAVHSKDNYKRV
          CLV.KGL...I..V.FNG.AECY..ANA.EP..CQK.PFNLDDPYPLLVVN.GSGVSILAVHSKD.YKR.
Retrocopy CLV<KGLAV<I*TVGFNGHAECYCLANATEPQQCQKIPFNLDDPYPLLVVNTGSGVSILAVHSKDIYKRM

Parental  TGTSLGGGTFLGLCSLLTGCESFEEALEMA-SKGDSTQA
          TGTSLG.GTFLGLCSLLTGC.SFEEALEMA.SKGDSTQA
Retrocopy TGTSLGEGTFLGLCSLLTGCKSFEEALEMA>SKGDSTQA

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_2975 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 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011633	4 retrocopies	retro_chof_1188, retro_chof_1391, retro_chof_1837, retro_chof_830,
Callithrix jacchus	ENSCJAG00000015550	1 retrocopy	retro_cjac_2037,
Homo sapiens	ENSG00000120137	1 retrocopy	retro_hsap_779,
Gorilla gorilla	ENSGGOG00000004947	1 retrocopy	retro_ggor_646,
Nomascus leucogenys	ENSNLEG00000004896	5 retrocopies	retro_nleu_1430, retro_nleu_144, retro_nleu_2975 , retro_nleu_3058, retro_nleu_3099,
Pongo abelii	ENSPPYG00000016024	1 retrocopy	retro_pabe_2848,
Pan troglodytes	ENSPTRG00000017509	1 retrocopy	retro_ptro_608,
Tursiops truncatus	ENSTTRG00000016157	3 retrocopies	retro_ttru_1947, retro_ttru_29, retro_ttru_994,