RetrogeneDB ID: retro_nleu_1753

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397307.1:11716854..11717645(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMG2
• Ensembl ID: ENSNLEG00000009063
• Aliases: None
• Description: None

Sequence

>retro_nleu_1753
ATGTTCGTTCCATGCGGGGAGTCATCCCCTGACCTTGCCGGCTTCACCTTCCTAATGCCAGCAGTATCTGTTGGAAATGT
CGGCCAGCTTGCAACGGATCTGATTATTTCTACACTGAATATGTCTAAGATTGGTTCTTCTATACCGATTGTCTTGTGCC
AATAGTTGGAAACAATCCATATGCGACCGCAGAAGGAAATTCAACAAAACTTAGTATAAATGCTGAAGTATATTCATTGC
CTTCAAGAAAGCTGGTGGCTTTTCAGTTAAGATCCATTTTTATTAAGTATAAATCGAAGCCATTCTGTGAAAAACTGCTT
TCCTTGGTGAAAAGTAGTGGCTGTGCCAGTGTCATTGTTCTTTCTAGCAGTCATTCATATCAGCGTAATGATCTGCAGCT
TCGTAGTACTCCCTTCTGGTACCTACTTACACCTTCCATGCAAAAAAGTGTTCAAAATAAAATAAAGAGCCTTAACTGGC
AAGAGATGGAAAAAAGCTGGTGCATTCCTGAAATAGATGATTCCGAGTTTTGTATCCACATTCTGGGAGGAGGTATCACA
AAAACACTCAATGATGAAAGCTGTTCTAAAGAAATCCGAATGGCAGTTCTGCTGAAATTTGTTTTGGAAGGGGACAACAT
CCCAGATGCATTAGGTCTTGTTAAGTATCTTAATGAGTGTCTTCAGATAATCAAACCACTTAATGATGACCCCACAGCAT
CTACCTCACTGTAGAAAATACCAAGGTCTTGGAAATTACTATTTGGCAGTGGTCTTCCGCCTGCACTTTTT

Alignment

ORF - retro_nleu_1753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFVPCGESAPDLAGFTLLMPAVSVGNVGQLTMDLIISTLNMSKIG-YFYTDCLVPMVGNNPYATAEGNST
          MFVPCGES.PDLAGFT.LMPAVSVGNVGQL..DLIISTLNMSKIG..FYTDCLVP.VGNNPYATAEGNST
Retrocopy MFVPCGESSPDLAGFTFLMPAVSVGNVGQLATDLIISTLNMSKIG<FFYTDCLVPIVGNNPYATAEGNST

Parental  ELSINAEVYSLPSRKLVALQLRSIFIKYKSKPFCEKLLSWVKSSGCARVIVLSSSHSYQRNDLQLRSTPF
          .LSINAEVYSLPSRKLVA.QLRSIFIKYKSKPFCEKLLS.VKSSGCA.VIVLSSSHSYQRNDLQLRSTPF
Retrocopy KLSINAEVYSLPSRKLVAFQLRSIFIKYKSKPFCEKLLSLVKSSGCASVIVLSSSHSYQRNDLQLRSTPF

Parental  RYLLTPSMQKSVQNKIKSLNWQEMEKSRCIPEIDDSEFCIRIPGGGITKTLYDESCSKEIQMAVLLKFVS
          .YLLTPSMQKSVQNKIKSLNWQEMEKS.CIPEIDDSEFCI.I.GGGITKTL.DESCSKEI.MAVLLKFV.
Retrocopy WYLLTPSMQKSVQNKIKSLNWQEMEKSWCIPEIDDSEFCIHILGGGITKTLNDESCSKEIRMAVLLKFVL

Parental  EGDNIPDALGLVEYLNEWLQIIKPLSDDPTASASRWKIPSSWRLLFGSGLPPALF
          EGDNIPDALGLV.YLNE.LQIIKPL.DDPTAS.S..KIP.SW.LLFGSGLPPALF
Retrocopy EGDNIPDALGLVKYLNECLQIIKPLNDDPTASTSL*KIPRSWKLLFGSGLPPALF

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_1753 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018855	1 retrocopy	retro_cfam_424,
Choloepus hoffmanni	ENSCHOG00000010042	1 retrocopy	retro_chof_1738,
Myotis lucifugus	ENSMLUG00000017744	1 retrocopy	retro_mluc_2496,
Macaca mulatta	ENSMMUG00000021855	1 retrocopy	retro_mmul_198,
Nomascus leucogenys	ENSNLEG00000009063	1 retrocopy	retro_nleu_1753 ,
Oryctolagus cuniculus	ENSOCUG00000005086	1 retrocopy	retro_ocun_1448,
Sus scrofa	ENSSSCG00000021827	2 retrocopies	retro_sscr_1008, retro_sscr_763,