RetrogeneDB ID: retro_nleu_649

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397269.1:33787236..33788247(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000006046
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSDL2
• Ensembl ID: ENSNLEG00000016534
• Aliases: None
• Description: None

Sequence

>retro_nleu_649
ATGTTACCCAACACCGGGAGGCTGGCAGGATGTACAGTTTTTATCACAGGTGCAAGCTGTGGCATTGGCAAAGCTATTGC
ATTGAAAGCAGCAAAGGATGGAGCAAATATTGTTATTGCTGCAAAGACCGCCCAGCCACATCCAAAACTTCTAGGCACAA
TCTATACTGCTGCTGAAGAAATTGAAGCAGTTGGAGGAAAGGTCTTGCCATGTATTGTTGATGTGAGAGATGAACAGCAG
ATCAGTGCTGCAGTGGAGAAAGCCATCAAGAAATTTGGAGGAATTGATATTCTGGCAAATAATGCCAGTGCCATTAGTTT
GACCAACACATTGGACACACCTACCAAGAGACTGGATCTGATGATGAATGTGAAAACCAGAGGCACCTACCTTGCATCTA
AAGCATGTATTCCTTATTTGAAAAAGAGTAAAGTTGCTCATATCCTTAATATCAGTCCACCACTGAACCTAAATCCAGTT
TGGTTCAAACAGCACTGTGCTTATACCATTGCTAAGTATGGTATGTCGATGTATGTGCTTGGAATGGCAGAAGAATTTAA
AGGTGAAATTGCAGTCAATGCATTATGGCCTAAAACAACCATACACACTGCTGCTATGGATATGCTGGGAGGACCTGGTA
TCGAAAGCCAGTGTAGAAAAGTTGATATCATTGCAGATGCAGCATATTCCATTTTCCAAAAGCCAAAAAGTTTTACTGGC
AACTTTGCCATTGACGAAAATATCTTAAAAGAAGAAGGAATAGAAAAATTTGATGTTTATGCAATTAAACCAGGTCATCC
TCTGCAACCAGATTTCTTCTTAGATGAGTACCCAGAAGCAGTTAGCAAGAAAATGGAATCAACTGGTGCTGTTCCAGAAT
TCAAAGAACAGAAACCACAGATGCAACCAAAACCACGTTCTGGAGCTCTGGAAGAAACATTTAGAATTGTTAAGGATTAT
CTCAGTGATGATGTAGTTAAAGCCACTCAAGCAATCTATCTGTTTGAACTC

Alignment

ORF - retro_nleu_649 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.14 %
• Parental protein coverage: 80.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLPNTGRLAGCTVFITGASRGIGKAIALKAAKDGANIVIAAKTAQPHPKLLGTIYTAAEEIEAVGGKALP
          MLPNTGRLAGCTVFITGAS.GIGKAIALKAAKDGANIVIAAKTAQPHPKLLGTIYTAAEEIEAVGGK.LP
Retrocopy MLPNTGRLAGCTVFITGASCGIGKAIALKAAKDGANIVIAAKTAQPHPKLLGTIYTAAEEIEAVGGKVLP

Parental  CIVDVRDEQQISAAVEKAIKKFGGIDILVNNASAISLTNTLDTPTKRLDLMMNVNTRGTYLASKACIPYL
          CIVDVRDEQQISAAVEKAIKKFGGIDIL.NNASAISLTNTLDTPTKRLDLMMNV.TRGTYLASKACIPYL
Retrocopy CIVDVRDEQQISAAVEKAIKKFGGIDILANNASAISLTNTLDTPTKRLDLMMNVKTRGTYLASKACIPYL

Parental  KKSKVAHILNISPPLNLNPVWFKQHCAYTIAKYGMSMYVLGMAEEFKGEIAVNALWPKTAIHTAAMDMLG
          KKSKVAHILNISPPLNLNPVWFKQHCAYTIAKYGMSMYVLGMAEEFKGEIAVNALWPKT.IHTAAMDMLG
Retrocopy KKSKVAHILNISPPLNLNPVWFKQHCAYTIAKYGMSMYVLGMAEEFKGEIAVNALWPKTTIHTAAMDMLG

Parental  GPGIESQCRKVDIIADAAYSIFQKPKSFTGNFVIDENILKEEGIENFDIYAIKPGHPLQPDFFLDEHPEA
          GPGIESQCRKVDIIADAAYSIFQKPKSFTGNF.IDENILKEEGIE.FD.YAIKPGHPLQPDFFLDE.PEA
Retrocopy GPGIESQCRKVDIIADAAYSIFQKPKSFTGNFAIDENILKEEGIEKFDVYAIKPGHPLQPDFFLDEYPEA

Parental  VSKKMESTGAVPEFKEEKPQPQPKPRSGAVEETFRIVKDSLSDDVVKATQAIYLFEL
          VSKKMESTGAVPEFKE.KPQ.QPKPRSGA.EETFRIVKD.LSDDVVKATQAIYLFEL
Retrocopy VSKKMESTGAVPEFKEQKPQMQPKPRSGALEETFRIVKDYLSDDVVKATQAIYLFEL

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_649 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006832	1 retrocopy	retro_amel_1368,
Canis familiaris	ENSCAFG00000003028	1 retrocopy	retro_cfam_480,
Nomascus leucogenys	ENSNLEG00000016534	1 retrocopy	retro_nleu_649 ,
Ictidomys tridecemlineatus	ENSSTOG00000012222	1 retrocopy	retro_itri_471,
Tupaia belangeri	ENSTBEG00000013420	2 retrocopies	retro_tbel_2324, retro_tbel_3321,