RetrogeneDB ID: retro_nleu_221

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:49121116..49122288(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC1
• Ensembl ID: ENSNLEG00000003142
• Aliases: None
• Description: None

Sequence

>retro_nleu_221
ATTGATAATAAAGCACTGTATGATACACTTTCTGCTTTTGGTAACATCCTTTCATGTAAGGTGGGCTGTGATGAAAATGA
TTCCAAGGGCTATGGATTTGTACACTTTGAGACACAGGAAGCAGCTGAAAGAGCGATGGAAAAAATGAATGGAATGCTCC
TAAATGATCGCAAAGTATTTGTTGGACGATTTACGTCTCATAAAGAACGAGAAGCTGAACTTGGAGCTACCCGAAAGGGT
TCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGCGCCTTAAGGATCTCTTCAGCAAGTTTGGGCGT
GCCTTAAATGTGAAAGTAATGACTGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGGCTTGAAGA
TGCACAGAAAGCTGTAGATGAAATGAATGGAAAGGAGCTCAATGGAAAACAAATTTATGTTGGTAGAGCTCACAAAAAAG
GGGAAGGGCAGACAGAACTTAAGCGCAAATTTGAACAGATGAAGCAAGATAGGATCACCAGATACCACGGTGTTAATCTT
TATGTGAAAAATCTTGATGATGGCATTGATCATTAACATCTTCGGAAAGAGTTTTCTCCGTTTGGTACAATCACTAGTGC
AAAGGTTATGATGGAGGGTGGTCATAGCAAAGGGTTTGGTTTTGTATGTTTCTCCTCACCAGAAGAAGCCACTAAAGCAG
TTACAGAAATGAATGGTAGAGTTGTGGCCACAAAGCCATTGTATGTCGCTTTAGCTCAGTGCAAAGAAGAGTGCCAGGCT
CACCTCACTAACCAGTATATGCAAAGAATGGCAAGTGTACGAGCTGTGCCCAATCTTGTAATCAACCCCTACCAGCCAGC
ACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAGACTCAGAACAGTGCTGCATATTATCCTCCTAGCCAAATTGCTC
AACTAAGACCAATTCCTCACTGGACTGCTCAGGGTGCCAGACCCCATCCATTCCAAAATATGTCCAGTGCTATCCACCCA
GCTGCTCCTAGACCACCGTTTAGTACTATGAGACCAGCTTCTTCACAGGTTCCATGAGTTATGTCAACGCAGCGTGTTGC
TAACACATCAACACAGACAATGGGTCCATGTCCTGCAGCTGCTGCTGCTGCA

Alignment

ORF - retro_nleu_221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.33 %
• Parental protein coverage: 61.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER
          IDNKALYDT.SAFGNILSCKV.CDEN.SKGYGFVHFETQEAAERA.EKMNGMLLNDRKVFVGRF.S.KER
Retrocopy IDNKALYDTLSAFGNILSCKVGCDENDSKGYGFVHFETQEAAERAMEKMNGMLLNDRKVFVGRFTSHKER

Parental  EAELGARAKE-FTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAV
          EAELGA..K..FTNVYIKNFGEDMDDERLKDLF.KFG.AL.VKVMTDESGKSKGFGFVSFER.EDAQKAV
Retrocopy EAELGATRKG<FTNVYIKNFGEDMDDERLKDLFSKFGRALNVKVMTDESGKSKGFGFVSFERLEDAQKAV

Parental  DEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFG
          DEMNGKELNGKQIYVGRA.KK.E.QTELKRKFEQMKQDRITRY.GVNLYVKNLDDGID...LRKEFSPFG
Retrocopy DEMNGKELNGKQIYVGRAHKKGEGQTELKRKFEQMKQDRITRYHGVNLYVKNLDDGIDH*HLRKEFSPFG

Parental  TITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMAS
          TITSAKVMMEGG.SKGFGFVCFSSPEEATKAVTEMNGR.VATKPLYVALAQ.KEE.QAHLTNQYMQRMAS
Retrocopy TITSAKVMMEGGHSKGFGFVCFSSPEEATKAVTEMNGRVVATKPLYVALAQCKEECQAHLTNQYMQRMAS

Parental  VRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAA
          VRAVPN.VINPYQPAPPSGYFMAAIPQTQN.AAYYPPSQIAQLRP.P.WTAQGARPHPFQNM..AI.PAA
Retrocopy VRAVPNLVINPYQPAPPSGYFMAAIPQTQNSAAYYPPSQIAQLRPIPHWTAQGARPHPFQNMSSAIHPAA

Parental  PRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAAAAAA
          PRPPFSTMRPASSQVP.VMSTQRVANTSTQTMGP.PAAAAAA
Retrocopy PRPPFSTMRPASSQVP*VMSTQRVANTSTQTMGPCPAAAAAA

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_221 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 15 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys	ENSNLEG00000003142	3 retrocopies	retro_nleu_221 , retro_nleu_2412, retro_nleu_611,
Nomascus leucogenys	ENSNLEG00000011928	2 retrocopies	retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,