RetrogeneDB ID: retro_nleu_1643

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397302.1:20510784..20511274(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD53
• Ensembl ID: ENSNLEG00000003649
• Aliases: None
• Description: None

Sequence

>retro_nleu_1643
GGGATGTACCCGCTGATCCACAACAGCTTGTGAGTGCTCTTCCATAAGCTCCCCTCCCTCACGCTGGGCAATGTGCTTGT
CATCGTGGGCTCCATGATCACGGTGGTGGCCTTCCTGGGCTGCATAGGCTCTGTCAAGAAAAACAGTGCCTGCTTATGTC
CTTGTTCATTCTGCTGCCGATTATCCTCCTTGCTGAGGTGACCTTGGCCATCCTGCACTTCGTTTACGAACAGAAGCTGA
ATGTATAGGTAGCTGAGGGCCTGACGGACAGCATCTACCATTACCACTGGGACAACAGCACCAGGCGATGTGGGACTCTA
TCCAGTCATTTCTGAACTGTTGTGGCGTAAATGGCACGAGTGATTGGTCCAGCGGGCAACAAGCATCTTGACCCTCAGAT
CCAAAAGTGAAAGGTTGCTATGCAAAAGTGAGACTGTAGTTTCACACCAATTTCCTGTATATCAGAATCATCACTATCTG
TGTATATGTG

Alignment

ORF - retro_nleu_1643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.9 %
• Parental protein coverage: 74.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GIYLLIHNNFGVLFHNLPSLTLGNVFVIVGSIIMVVAFLGCMGSIKEN-KCLLMSFFILLLIILLAEVTL
          G.Y.LIHN...VLFH.LPSLTLGNV.VIVGS.I.VVAFLGC.GS.K.N..CLLMS.FILL.IILLAEVTL
Retrocopy GMYPLIHNSL*VLFHKLPSLTLGNVLVIVGSMITVVAFLGCIGSVKKN<QCLLMSLFILLPIILLAEVTL

Parental  AILLFVYEQKLNEYVAKGLTDSIHRYHSDNSTK-AAWDSIQSFLRCCGINGTSDWTSSPPASCPSDPKVE
          AIL.FVYEQKLN..VA.GLTDSI..YH.DNST..A.WDSIQSFL.CCG.NGTSDW.S...AS.PSDPKV.
Retrocopy AILHFVYEQKLNV*VAEGLTDSIYHYHWDNSTR<AMWDSIQSFLNCCGVNGTSDWSSGQQAS*PSDPKVK

Parental  GCYAKARLWFHSNFLYIGIVTICVCV
          GCYAK.RL.FH.NFLYI.I.TICV.V
Retrocopy GCYAKVRL*FHTNFLYIRIITICVYV

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_1643 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010760	2 retrocopies	retro_chof_116, retro_chof_307,
Homo sapiens	ENSG00000143119	1 retrocopy	retro_hsap_2960,
Gorilla gorilla	ENSGGOG00000005468	1 retrocopy	retro_ggor_2050,
Macaca mulatta	ENSMMUG00000000811	1 retrocopy	retro_mmul_1894,
Nomascus leucogenys	ENSNLEG00000003649	1 retrocopy	retro_nleu_1643 ,
Nomascus leucogenys	ENSNLEG00000007505	1 retrocopy	retro_nleu_1186,
Otolemur garnettii	ENSOGAG00000016713	2 retrocopies	retro_ogar_2407, retro_ogar_469,
Pan troglodytes	ENSPTRG00000001085	1 retrocopy	retro_ptro_2004,