RetrogeneDB ID: retro_nleu_1640

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397302.1:16705992..16706801(+)
• Located in intron of: ENSNLEG00000009160

Retrocopy information

• Ensembl ID: ENSNLEG00000009170
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDHB
• Ensembl ID: ENSNLEG00000013264
• Aliases: None
• Description: None

Sequence

>retro_nleu_1640
CGCCGGTTACCGGCCGCAACCCTTGGCGGAGCCTGCCTGCAGGCCTCCTGAGGAGCCCAGACAGCTGCAGCCGCAGCTGC
CCGTATCAAGAAATTTGCCATCTATCGATGGGACCCAGACAAGGCTGGAGACAAACCTCATATGCAGACTTATGAAGTTG
ACCTTAATAAACGTGGCCCCATGGTATTGGATGCTTTAATCAAGATTAAGAATGAAGTTGACTCTACTTTGACCTTCCGA
AGATCATGCAGAGAAGGCATCTGTGGCTCTTGTGCATGAACATCAATGGAGGCAACACTCTAGTTTGCACCCGAAGGATT
GACACCAACCTCAGTAAGGTCTCAAAAATCTACCCTCTTCCACACATGTATGTGATAAAGGATCTTGTTCCCGATTTGAG
CAACTTCTATGCACAATACAAATTCATTGAGCCTTATTTGAAGAAGAAGGATGAATCTCAGGAAGGCAAGCAGCAGTATC
TGCAGTCCATAGAAGAGCGTGAGAAACTGGACGGGCTCTACGAGTGCATTCTCTGTGCCTGCTGTAGCACCAGCTGCCCC
AGCTACTGGTGAAACAGAGACAAATATCTGGGGCCTGCAGTTCTTATGCAGGCCTATCGCTGGATGATTGACTCCAGAGA
CGACTTCACAGAGGAGCGCCTGGCCAAGCTGCAGGACCCATTCTCGCTATACTGCTGCCACACCATCATGAACTGCACAA
GGACCTGTCCTAAGGGTCTGAATCCAGAGAAAGCTATTGCGGAGATCAAGAAAATGATGGCAACCTATAAGGAGAAGAAA
GCTTCAGTT

Alignment

ORF - retro_nleu_1640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.46 %
• Parental protein coverage: 96.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRLPATTLSGACLQASRGAQTAAAAAPRIKKFAIYRWDPDKAGDKPHMQTYEVDLNKCGPMVLDALIKIK
          RRLPA.TL.GACLQAS.GAQTAAAAA.RIKKFAIYRWDPDKAGDKPHMQTYEVDLNK.GPMVLDALIKIK
Retrocopy RRLPAATLGGACLQAS*GAQTAAAAAARIKKFAIYRWDPDKAGDKPHMQTYEVDLNKRGPMVLDALIKIK

Parental  NEVDSTLTFRRSCREGICGSCA-MNINGGNTLACTRKIDTNLNKVSKIYPLPHMYVIKDLVPDLSNFYAQ
          NEVDSTLTFRRSCREGICGSCA.MNINGGNTL.CTR.IDTNL.KVSKIYPLPHMYVIKDLVPDLSNFYAQ
Retrocopy NEVDSTLTFRRSCREGICGSCA<MNINGGNTLVCTRRIDTNLSKVSKIYPLPHMYVIKDLVPDLSNFYAQ

Parental  YKSIEPYL-KKDESQEGKQQYLQSIEEREKLDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRWM
          YK.IEPYL.KKDESQEGKQQYLQSIEEREKLDGLYECILCACCSTSCPSYW.N.DKYLGPAVLMQAYRWM
Retrocopy YKFIEPYLKKKDESQEGKQQYLQSIEEREKLDGLYECILCACCSTSCPSYW*NRDKYLGPAVLMQAYRWM

Parental  IDSRDDFTEERLAKLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKMMATYKEKKASV
          IDSRDDFTEERLAKLQDPFSLY.CHTIMNCTRTCPKGLNP.KAIAEIKKMMATYKEKKASV
Retrocopy IDSRDDFTEERLAKLQDPFSLYCCHTIMNCTRTCPKGLNPEKAIAEIKKMMATYKEKKASV

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_1640 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015832	1 retrocopy	retro_cfam_587,
Choloepus hoffmanni	ENSCHOG00000005664	1 retrocopy	retro_chof_2016,
Callithrix jacchus	ENSCJAG00000007927	1 retrocopy	retro_cjac_2988,
Loxodonta africana	ENSLAFG00000018475	1 retrocopy	retro_lafr_454,
Macropus eugenii	ENSMEUG00000004817	1 retrocopy	retro_meug_1106,
Microcebus murinus	ENSMICG00000016629	1 retrocopy	retro_mmur_1062,
Myotis lucifugus	ENSMLUG00000000032	1 retrocopy	retro_mluc_150,
Nomascus leucogenys	ENSNLEG00000013264	1 retrocopy	retro_nleu_1640 ,
Sorex araneus	ENSSARG00000013780	1 retrocopy	retro_sara_577,
Tupaia belangeri	ENSTBEG00000004803	2 retrocopies	retro_tbel_2480, retro_tbel_2875,
Xenopus tropicalis	ENSXETG00000013435	1 retrocopy	retro_xtro_60,