RetrogeneDB ID: retro_nleu_3030

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397596.1:306728..307708(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MBD1
• Ensembl ID: ENSNLEG00000011661
• Aliases: None
• Description: None

Sequence

>retro_nleu_3030
ATGGCTGAGGACTGGCTGGACTGCCCGGCCCTGGGCCCTGGCTGGAAGCGCTGTGAAGTCTTTCGCAAGTCAGGGGCCAC
CTGTGGACGCTCAGACACCTGTTACCAGAGCCCCACAGGAGACAGGATCTGAAGCAAAGTTGAGCTGACTCGATACCTGG
GCCCTGCGTGTGATCTCACCCTCTTCGACTTCAAACAAGGCATCTTGTGCTATCCAGCCCCCAAGGCCCATCCCGTGGCG
GTTGCCAGCAAGAAGCGAAAGAAGCATTCAAGGCTAGCCAAAACCCAGAAACGTCAGGTTGGACCCCCGAGTGGTGAGGT
CAGGAAGGAGGCCCCGAAGGATGAGACCAAGGCTAACACTGACACAGCCCCAGCTTCATTCCCTGCTCCTGGATGCTGTG
AGAACTGTGGAATCAGCTTCCCAGGGGATGGCACCCAAAGGCAGCGGCTCAAAACGTTGTGCAAAGACTGTCGAGCACAG
AGAATTGCCTTCAACCGGGAACAGAGAATATTTAAGCGTGTGAGCTCTGGGGAGTGTGCAGCCTGCCAGGTAACAGAAGA
CTGTGGGGCCTGCTCCACCTGCCTCCTGCAGCTGCCCCATGATGTGGCATCGGGGCTGTTCTGCAAGTGTGAACGGAGAC
GCTGCCTCCGGATTGTGGAAAGCAGCCGAGGGTGTGGAGTATGCCGGGGCTGTCAGACCCAAGAGGATTGTGGCCTTTGC
CCCATCTGCCTTCGCCCTCCCCGCCCTGGTCTCAGGCACCAGTGGAAATGTGTCCAGAGACGTTGCCTACGGGGTAAACA
TGCCCCCCCAAGGGAGGCTGTGACTCCAAGATGGCTGCCAGGCGGCGCCCCGGAGCCCAGCCACTGCCTCCACCACCCCC
ATCACAGTCCCCAGAGCCCACAGAGCCGCACCCCAGAGCCCTGGCCCCCTCACCACCTGCCGAGTTCATCTATTACTGTG
TAGACGAGGACGAGCTAAAG

Alignment

ORF - retro_nleu_3030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 54.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEDWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLTLFDFKQGILC
          MAEDWLDCPALGPGWKR.EVFRKSGATCGRSDT.YQSPTGDRI.SKVELTRYLGPACDLTLFDFKQGILC
Retrocopy MAEDWLDCPALGPGWKRCEVFRKSGATCGRSDTCYQSPTGDRI*SKVELTRYLGPACDLTLFDFKQGILC

Parental  YPAPKAHPVAVASKKRKKPSRPAKTRKRQVGPQSGEVRKEAPRDETKADTDTAPASFPAPGCCENCGISF
          YPAPKAHPVAVASKKRKK.SR.AKT.KRQVGP.SGEVRKEAP.DETKA.TDTAPASFPAPGCCENCGISF
Retrocopy YPAPKAHPVAVASKKRKKHSRLAKTQKRQVGPPSGEVRKEAPKDETKANTDTAPASFPAPGCCENCGISF

Parental  SGDGTQRQRLKTLCKDCRAQRIAFNREQRMFKRVGCGECAACQVTEDCGACSTCLLQLPHDVASGLFCKC
          .GDGTQRQRLKTLCKDCRAQRIAFNREQR.FKRV..GECAACQVTEDCGACSTCLLQLPHDVASGLFCKC
Retrocopy PGDGTQRQRLKTLCKDCRAQRIAFNREQRIFKRVSSGECAACQVTEDCGACSTCLLQLPHDVASGLFCKC

Parental  ERRRCLRIVERSRGCGVCRGCQTQEDCGRCPICLRPPRPGLRRQWKCVQRRCLRGKHA-RRKGGCDSKMA
          ERRRCLRIVE.SRGCGVCRGCQTQEDCG.CPICLRPPRPGLR.QWKCVQRRCLRGKHA...KGGCDSKMA
Retrocopy ERRRCLRIVESSRGCGVCRGCQTQEDCGLCPICLRPPRPGLRHQWKCVQRRCLRGKHA<PPKGGCDSKMA

Parental  ARRRPGSQALPPPPPSQSPEPTEPHPRALAPSPPAEFIYYCVDEDELQ
          ARRRPG.Q.LPPPPPSQSPEPTEPHPRALAPSPPAEFIYYCVDEDEL.
Retrocopy ARRRPGAQPLPPPPPSQSPEPTEPHPRALAPSPPAEFIYYCVDEDELK

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_3030 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004959	1 retrocopy	retro_cjac_1830,
Monodelphis domestica	ENSMODG00000010534	1 retrocopy	retro_mdom_217,
Nomascus leucogenys	ENSNLEG00000011661	1 retrocopy	retro_nleu_3030 ,