RetrogeneDB ID: retro_nleu_138

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: ADFV01136183.1:14845..15937(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CXADR
• Ensembl ID: ENSNLEG00000002063
• Aliases: None
• Description: None

Sequence

>retro_nleu_138
ATGGCGCTCCTGCTGCGCTTCGTGCTCCTGTGCGGAGTCGCGAATTTCGCCAGAAGTTTGAGTATCACTACTCCTGAAGA
GATGATTGAAAAAGCCAAAGGGGAAACTGCCTATCTGCCATGCAAATTTACGCTGAGCCCGGAAGACCAGGGACCGCTGG
ACATCTAGTGGCTGATATCAACAGCTGATAATCAGTAGGTGGATCAAGTGATTATTTTATATTCTGGAGACAAAATTTAT
GATGACAACTATCCAGATCTGAAAGGCCGAGTACATTTTACGAGTAATGATCTCCAATCTGGTGCTGCATCAATAAATGT
AACGAATTTACAGCTGTCAGATATTGGCAAGTATCAGTGCAAAGTGAAAAAAGCTCCTGGTGTTGCAAATAAGAAGATTC
ATCTGGTAGTTCTTGTTAAGCCTTCAGGTGCAAGATGTTACGTTGATGGATCAGAAGAAATTGGAAATGACTTTAAACTA
AAATGTGAACCAAAAGAAGGTTCACTTCCATTACAGTATGAGTGGCAAAAATTGTCTGACTCACAGAAAATGCCCACTTC
ATGGTTAGCAGAAATGACTTCATCTGTTATATCTGTAAAAAATGCCTCTTCTGAGTACTCTGGGACATACAGCTGTACAG
TCAGAAACAGAGTGGGCTCTGATCCGTGCCTGCTGCGTCTAAACGTTGTCCCTCCTTCAAATAAAGCTGGACTAATTGCA
GGAGCCATTATAGGAACTTTGCTTGCTCTAGCGCTCATTGGTCTTATCTTTTGCTGTCGTAAAAAGCGCAGAGAAGAAAA
ATATTAAAAGGAAGTTCATCACCATATCAGGGAAGATGTGCTGCCTCCAAAGAGCCGTACGTCCACTGCCAGAAGCCACA
TCGGTAGTAATCATTCATCCCTGGGATCCATGTCTCCTTCCAACATGGAAGGATATTCTAAGACTCAGTATAACCAAGTA
CCAGGTGAAGACTTTGAACGCGCTCCTCAGAGTCCGACTCTCCCACCTGCTAAGGTAGCTGCCCCTAATCTAAGTCGAAT
GGGCGCGATTCCTGTGATGATTCCAGCACAGAGCAAGGATGGGTCTATAGTA

Alignment

ORF - retro_nleu_138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFLLRFVLLYGVVDFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
          MA.LLRFVLL.GV..FARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDI.WLIS.ADNQ.VDQV
Retrocopy MALLLRFVLLCGVANFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDI*WLISTADNQ*VDQV

Parental  IILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVK
          IILYSGDKIYDD.YPDLKGRVHFTSNDL.SG.ASINVTNLQLSDIG.YQCKVKKAPGVANKKIHLVVLVK
Retrocopy IILYSGDKIYDDNYPDLKGRVHFTSNDLQSGAASINVTNLQLSDIGKYQCKVKKAPGVANKKIHLVVLVK

Parental  PSGARCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISVKNASSEYSGTY
          PSGARCYVDGSEEIG.DFKLKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISVKNASSEYSGTY
Retrocopy PSGARCYVDGSEEIGNDFKLKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISVKNASSEYSGTY

Parental  SCTVRNRVGSDQCLLRLNVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDIRED
          SCTVRNRVGSD.CLLRLNVVPPSNKAGLIAGAIIGTLLALALIGL.IFCCRKKRREEKY.KEVHH.IRED
Retrocopy SCTVRNRVGSDPCLLRLNVVPPSNKAGLIAGAIIGTLLALALIGL-IFCCRKKRREEKY*KEVHHHIRED

Parental  VPPPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYNQVPSEDFERTPQSPTLPPAKVAAPNLSRMGA
          V.PPKSRTSTARS.IGSNHSSLGSMSPSNMEGYSKTQYNQVP.EDFER.PQSPTLPPAKVAAPNLSRMGA
Retrocopy VLPPKSRTSTARSHIGSNHSSLGSMSPSNMEGYSKTQYNQVPGEDFERAPQSPTLPPAKVAAPNLSRMGA

Parental  IPVMIPAQSKDGSIV
          IPVMIPAQSKDGSIV
Retrocopy IPVMIPAQSKDGSIV

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_138 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 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012975	1 retrocopy	retro_dnov_990,
Homo sapiens	ENSG00000154639	6 retrocopies	retro_hsap_1533, retro_hsap_1535, retro_hsap_1918, retro_hsap_2492, retro_hsap_4322, retro_hsap_4323,
Nomascus leucogenys	ENSNLEG00000002063	2 retrocopies	retro_nleu_138 , retro_nleu_58,
Pongo abelii	ENSPPYG00000011295	2 retrocopies	retro_pabe_1273, retro_pabe_2776,
Pan troglodytes	ENSPTRG00000013795	4 retrocopies	retro_ptro_1244, retro_ptro_1444, retro_ptro_801, retro_ptro_995,
Sarcophilus harrisii	ENSSHAG00000005309	1 retrocopy	retro_shar_252,