RetrogeneDB ID: retro_nleu_2044

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397324.1:2628805..2629808(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBP3
• Ensembl ID: ENSNLEG00000002639
• Aliases: None
• Description: None

Sequence

>retro_nleu_2044
CCATCGGTGACCAAAGACTTGACCATTCAAAGTCCAGCTCCCCAGAACACTGCTCGACATGGACACCGGTGTGATTGAAG
GTGGATTAAATATCACTCTCACCATCCAGCTACTTATGCATGGAAAGGAAGTTGGCAGTATCATCGGAAAGAAAGGAGAA
TCAGTTAAGAAGATGCGCCAGGAGAGTGGTGCACGTATCAACATCTCAGAAGGGAATTGTCCTGAGAGAATTATCACTTT
GGCTGGACCCGCTAATGCCATCTTCAAAGCCTTTGCTATGATCATTGACAAACTGGAAGAGGACATAAGCAGCTCTATGA
CCAATAGCACAGCTGCCAGTAGACCCCCGGTCACCCTGAGGCTGGTGGTCCCTGCTAGTCGGTGTGGCTCTCTCACTGGA
AAAGGTGGTTGCAAGATCAAGGAAATACAAGACAGTACAGGGGCTCAGGTCTAGGTGGCAGGGGATATGCTACCCAACTC
AACTGAGCAGGCCATCACTATTGCTGGCATTCCGCAATCCATCATTGAGTGTGTCAAACAGATCTGCGTGGTCATGTTGG
AGTGCCCCCCGAAGGGCGTGACCATCCCGTACCGGCCCAAGTGTTCCAGCTCTCCGGTCACCTTTGCAGGTGGTCAGGCC
TATACCATTCAAGGACAGTATACCATTCCACAGCCAGATTTGACCAAGCTGCACCAGTTGGCAATGCAACAGTCTCATTT
TCCCATGACGCATGGCAACACCGGATTCAGTGCAGGTTTGGATGCATCTGCTCAGACTACTTCTCATGAACTCACCATTC
CAAACGATTTGATTGGCTGCATAATCGGGCGTCAAGGCGCCAAAATCAATGAGATCCCTCAGATGTCTGGGGCGCAGATC
AAAATTGCGAACCCAGTGGAAGGATCTACTGATAGGCAGGTTACCATCACTGGATCTGCTGCCAGCATTAGCCTGGCTCA
ATATCTAATCAATGTCAGGCTTTCCTCAGAGACGGGTGGCATG

Alignment

ORF - retro_nleu_2044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.51 %
• Parental protein coverage: 95.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PHSTLSTLSHHPQPQFGRR-MESKVSEGGLNVTLTIRLLMHGKEVGSIIGKKGETVKKMREESGARINIS
          P..T.......P.PQ...R.M...V.EGGLN.TLTI.LLMHGKEVGSIIGKKGE.VKKMR.ESGARINIS
Retrocopy PSVTKDLTIQSPAPQNTAR>MDTGVIEGGLNITLTIQLLMHGKEVGSIIGKKGESVKKMRQESGARINIS

Parental  EGNCPERIVTITGPTDAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKI
          EGNCPERI.T..GP..AIFKAFAMI..K.EEDI..SM.NS.A.S.PPVTLRLVVPAS.CGSL.GKGG.KI
Retrocopy EGNCPERIITLAGPANAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASRCGSLTGKGGCKI

Parental  KEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPYRPKPASTPVIFA
          KEI..STGAQV.VAGDMLPNSTE.A.TI.G.P..II.CVKQICVVMLE.PPKG.TIPYRPK..S.PV.FA
Retrocopy KEIQDSTGAQV*VAGDMLPNSTEQAITIAGIPQSIIECVKQICVVMLECPPKGVTIPYRPKCSSSPVTFA

Parental  GGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNPAFPGLDASPPASTHELTIPNDLIGCIIGRQ
          GGQAYTIQGQY.IP.PD.LTKLHQLAMQQ..FP..........GLDAS.....HELTIPNDLIGCIIGRQ
Retrocopy GGQAYTIQGQYTIPQPD-LTKLHQLAMQQSHFPMTHGNTGFSAGLDASAQTTSHELTIPNDLIGCIIGRQ

Parental  GTKINEIRQMSGAQIKIANATEGSSERQITITGTPANISLAQYLINARLTSEVTGM
          G.KINEI.QMSGAQIKIAN..EGS..RQ.TITG..A.ISLAQYLIN.RL.SE..GM
Retrocopy GAKINEIPQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSETGGM

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_2044 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003648	1 retrocopy	retro_cpor_257,
Dipodomys ordii	ENSDORG00000003640	2 retrocopies	retro_dord_742, retro_dord_748,
Myotis lucifugus	ENSMLUG00000003074	1 retrocopy	retro_mluc_574,
Nomascus leucogenys	ENSNLEG00000002639	1 retrocopy	retro_nleu_2044 ,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Oryctolagus cuniculus	ENSOCUG00000002696	1 retrocopy	retro_ocun_1257,
Rattus norvegicus	ENSRNOG00000001245	1 retrocopy	retro_rnor_2656,
Sorex araneus	ENSSARG00000007629	1 retrocopy	retro_sara_414,
Tursiops truncatus	ENSTTRG00000015075	1 retrocopy	retro_ttru_1095,