RetrogeneDB ID: retro_nleu_1618

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397301.1:15908568..15909603(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16ORF88
• Ensembl ID: ENSNLEG00000012496
• Aliases: None
• Description: None

Sequence

>retro_nleu_1618
AAGTGGACTTCCGGGTCACGGCGGAGCCGGCTCTCACGTGGAGGCGGGGAAGTTTGGCCCACCGGAAGATCACTAAGACA
CACAAAGTAGACCTGGGCCCTGGGATCCCAGAGAAGAAAAAGAAGAAGAAAGTGGTCAAAGAACCAGAGACTCAATACTC
AATTTTGAACAATGATGATTACTTTGCCCATGTTTCTCCTATGAAAGCCACAGTCCCCTCTAAGAGTGTGGTGCACGGGC
AGGTACCTGAGATGCCTCTAGTGAAGAAAAAGAAGGAAGAGAAGGGTGTCAGCACCCTTTGCGAGGAGCACATAGAACCT
GAGACCACGCTGCGTGCCAGACCGACAGAGAATTCATTCAGCCCAAGGAACTAGAGGCTTGGCCACTTGGAGTTCCTCAG
TGGGGAGAAGAAAAAGAGGAAGTCACCTCTGGCCATGTCCCATACCTCTGGGGTGAAAATCTCCCCAGACCCCAGACACG
GTGAGGAGGAAACCAGAGTTGGCAAGAAGCTCAAAAAACATAAGAAGGAAAAAAGGGAGGCCCAGGACCCTACAGCTTTC
TCAGTCCAGGACCCTTGGTTCTGCGAGGTCGGGGATGCTGTGGACACTTGCTCAGTGGGGAAGGAGGGTGAGGAACAGGT
AGCCTTGGGGCAGAAGCGGAAGCACAAGGGCCCCAGGGAACACAGTAGGAAGGCGAAGAAGAAAAAAAAAAATCCACCAG
GAGGGAGACGCCCTCCCAGGCCACTCCAAGCCCTCCAGGTCCATGGAGAGCTGCCCTAGGAAATGAAGTAAAAAGAAGCC
AGTCAAAGTGGAGGCTCCGGAATACATCCCCATAGGAGATGGCCCTAAAACCCCCGCGAAGAAAAAGATGAAGTCCAAGA
AGTAGGTGAAGCAGCCAGTCATTGAGGAGCCGGCTCTGAAAAGGAAGAAAAAGAAAAGGAAAGAGAGTGGGGTAGCAGGA
GACCCTTGGAAGGAGGAAACAGACACGGACTTGGAGGTGGTGTTGGAAAAGAAAGGCAACATGGACCAGGCACAC

Alignment

ORF - retro_nleu_1618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.7 %
• Parental protein coverage: 66.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KWTSGSRRSGLSRGGGEISPTGM-ITKTHKVD--PGLPEKKKKKKVVKEPETRYSVLNNDDYFADVSPIR
          KWTSGSRRS.LSRGGGE..PTG..ITKTHKVD..PG.PEKKKKKKVVKEPET.YS.LNNDDYFA.VSP..
Retrocopy KWTSGSRRSRLSRGGGEVWPTGR<ITKTHKVDLGPGIPEKKKKKKVVKEPETQYSILNNDDYFAHVSPMK

Parental  ATSPSKSVAHGQAPEMPLVKKKKKKKKGVSTLCKKHVEPETTLPARWTEKSPSPRKQVLGHLEFLSGEKK
          AT.PSKSV.HGQ.PEMPLVKKKK..K.GVSTLC..H.EPETTL.AR.TE.S.SPR...LGHLEFLSGEKK
Retrocopy ATVPSKSVVHGQVPEMPLVKKKKEEK-GVSTLCEEHIEPETTLRARPTENSFSPRN*RLGHLEFLSGEKK

Parental  RKKSPLAMSHASGVKTSPDPRQGEEETRVGKKLKKHKKEKKGAQDPTAFLVQDPWVCEAREARDVGDSCS
          ..KSPLAMSH.SGVK.SPDPR.GEEETRVGKKLKKHKKEK..AQDPTAF.VQDPW.C...E..D..D.CS
Retrocopy KRKSPLAMSHTSGVKISPDPRHGEEETRVGKKLKKHKKEKREAQDPTAFSVQDPWFC---EVGDAVDTCS

Parental  VGKKDEKQAAL-GQKRKQKSPREYNGKVKKKKI-HQEGDVLPGHSKPSRSMESSPRKGSKKKPVKVEAPE
          VGK..E.Q.AL.G.......P....G........HQEGD.LPGHSKPSRSMES.PRK.SKKKPVKVEAPE
Retrocopy VGKEGEEQVAL>GRSGSTRAPGNTVGRRRXXXXXHQEGDALPGHSKPSRSMESCPRK*SKKKPVKVEAPE

Parental  YIPVSDDPKASAKKKMKSKKKVEQPVIEEPALKRKKKKKRKESGVAGDPWKEETDTDLEVVLEKKGNMDE
          YIP..D.PK..AKKKMKSKK.V.QPVIEEPALKR.KKKKRKESGVAGDPWKEETDTDLEVVLEKKGNMD.
Retrocopy YIPIGDGPKTPAKKKMKSKK*VKQPVIEEPALKR-KKKKRKESGVAGDPWKEETDTDLEVVLEKKGNMDQ

Parental  AH
          AH
Retrocopy AH

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_1618 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 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018032	2 retrocopies	retro_cfam_1557, retro_cfam_1763,
Callithrix jacchus	ENSCJAG00000009625	1 retrocopy	retro_cjac_3199,
Homo sapiens	ENSG00000103550	3 retrocopies	retro_hsap_3487, retro_hsap_4007, retro_hsap_979,
Gorilla gorilla	ENSGGOG00000005673	1 retrocopy	retro_ggor_2691,
Macaca mulatta	ENSMMUG00000002707	2 retrocopies	retro_mmul_1771, retro_mmul_798,
Nomascus leucogenys	ENSNLEG00000012496	2 retrocopies	retro_nleu_1618 , retro_nleu_551,
Otolemur garnettii	ENSOGAG00000010065	4 retrocopies	retro_ogar_1115, retro_ogar_1480, retro_ogar_1481, retro_ogar_2259,
Pongo abelii	ENSPPYG00000007151	3 retrocopies	retro_pabe_3293, retro_pabe_828, retro_pabe_920,
Pan troglodytes	ENSPTRG00000007836	3 retrocopies	retro_ptro_2360, retro_ptro_767, retro_ptro_924,