RetrogeneDB ID: retro_nleu_1925

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397316.1:15677153..15679143(+)
• Located in intron of: ENSNLEG00000009256

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2B1
• Ensembl ID: ENSNLEG00000013939
• Aliases: None
• Description: None

Sequence

>retro_nleu_1925
ATGACTGATTCCAGGTATTTCACAACCAATAAAAAAGGAGAAATATTTGAACTAAAAGCTGAACTCAACAATGAAAAGAA
TGAAAAGAGAAAGGAGGCTGTGAAGAAAGTGATTGCTGCTATGACCGTGGGGAAGGATGTTAGTTCTCTCTTTCCAGACG
TAGTGAACTGTATGCAGACTGACAATCTGGAACTAAAGAAGCTTGTGTGTCTCTACTTGATGAACTATGCCAAGAGTCAG
CCAGACATGGCCATCATGGCTGTAAACAGCTTTGTGAAGGATTGCGAAGATCCTAATACTTTGATTCGAGCCTCGGCAGT
CAGAACCATGGGGTGCATCCGGGTAGACAAAATTACAGAGTATCTCTGTGAGCCGCTCCGCAAGTGCTTGAAGGATGAGG
ATCCCTATGTTAGGAAAACAGCAGCAGTCTGTGTGGCAAAACTGCATGATATCAATGCCCAAATGGTGGAAGATCAGGGA
TTTCTGCATTCTCTACGGGATCTCATAGCAGATTCAAATCCAATGGTGGTGGCTAAGGCTGTAGCGGCATTATCTGAAAT
CAGTGAGTCTCACCCAAACAGCAACTTACTTGATCTGAACCCACAGAACATTAGTAAGCTGCTGACAGCCCTGAATGAAT
GCACTGAATGGGGCCAGATTTTCATCCTGGACTGCCTGTCTAATTATAACCCTAAAGATGATCAGGAGGCTCAGAGCATC
TCTGAGCGGGTAACTCCCTGGCTATCCCATGCCAACTCAGCAGTGGTGCTTTCAGAGGTAAAAGTCCTAATGAAGTTTCT
AGAATTGTTACCTAAGGATTCTGACTACTACAATATGCTGCTGAAGAAGTTAGCCCCTCCACTTGTCACTTTGCTGTCTG
GGGAGCCAGAAGTGCAGTATGTCGCCCTGAGGAACATCAACTTAATTGTCCAGAAAAGGCCTGAAATCTTGAAGCAGGAA
ATCAAAGTCTTCTTTGTGAAGTACAGTGATCCCATCTATGTTAAACTAGAGAAGTTGGACACCATGATTCGTTTGGCATC
TCAAGCCAACATTGCTCAGGTTCTGGCAGAACTGAAGGAATATGCCACAGAGGTGGATGTTGACTTTGTTCAAAAAGCTG
TGCGGGCCATTGAACGGTGTGCCATCAAGTGGAGCAATCTGCAGAGCGCTGTGTAAGCACATTGCTTGATCTAATCCAGA
CCAAAGTGAATTATGTGGTCCAAGAAGTGATTGTTGTCATCAGATCTTCCGCAAATACCCCAACAAGTATGAAAGTATCA
TTGCCACTCTATGTGAGAACTTAGACTCGCTGGATGAGCCAGATGCTCGAGCAGCTATGATTTGGATTGTGGGAGAATAT
GCTGAAAGAATTGACAATGTAGATGAGTTACTAGAAAGCTTCCTGGAGGGTTTTCACAATGAAAGCGCCCAGGTGCAGCT
CACTCTGCTTACTGCCATAGTGAAGCTATTTCTTAAGAAACCGTCAGAAACACAAGAGCTAGTCCAGCAGGTCTTGAGTT
TGGCAACACAGGATTCTGATAATCCTGACCTTTGAGACCGGGGCTATATTTATTGGCGCCTTCTCTCAACTGACCCTGTC
ACAGCTAAAGAAGTAGTCTTGTCTGAGAAGCCACTGATCTCTGAGGAGACGGACCTTATTGAGCCAACTCTGCTGGATGA
GCTAATCTGCCACATTGGTTCTTTGGCCTCTGTGTATCATAAGCCTCCCAATGCTTTTGTGGAAGGAAGTCATGGAATTC
ATCGTAAACACTTGCCAATTCATCATGGGAGCACTGATGCAGGTGACAGCCCTGTTGGCACTAGCACTGCAACAAACTTG
GAACAGCCTCAGGTTATCCCCTCTCAAGGTGATCTTCTAGGGGATCTTTTAAACCTTGACCTCGGTCCCCCAGTCAATGT
GCCACAGGTGTCCTCCATGCGGATGGGAGCAGTGGATCTCCTAGGAGGAGGACTAGATAGTCTAGTGGGA

Alignment

ORF - retro_nleu_1925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.35 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY
          MTDS.YFTTNKKGEIFELKAELNNEK.EKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLV.
Retrocopy MTDSRYFTTNKKGEIFELKAELNNEKNEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVC

Parental  LYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYLMNYAKSQPDMAIMAVNSFVKDCEDPN.LIRA.AVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
Retrocopy LYLMNYAKSQPDMAIMAVNSFVKDCEDPNTLIRASAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT

Parental  AAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTA
          AAVCVAKLHDINAQMVEDQGFL.SLRDLIADSNPMVVA.AVAALSEISESHPNSNLLDLNPQNI.KLLTA
Retrocopy AAVCVAKLHDINAQMVEDQGFLHSLRDLIADSNPMVVAKAVAALSEISESHPNSNLLDLNPQNISKLLTA

Parental  LNECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNML
          LNECTEWGQIFILDCLSNYNPKDD.EAQSI.ERVTP.LSHANSAVVLS.VKVLMKFLELLPKDSDYYNML
Retrocopy LNECTEWGQIFILDCLSNYNPKDDQEAQSISERVTPWLSHANSAVVLSEVKVLMKFLELLPKDSDYYNML

Parental  LKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQAN
          LKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKY.DPIYVKLEKLD.MIRLASQAN
Retrocopy LKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYSDPIYVKLEKLDTMIRLASQAN

Parental  IAQVLAELKEYATEVDVDFVRKAVRAIGRCAIK-VEQSAERCVSTLLDLIQTKVNYVVQEAIVVI-RDIF
          IAQVLAELKEYATEVDVDFV.KAVRAI.RCAIK.VEQSAERCVSTLLDLIQTKVNYVVQE...V....IF
Retrocopy IAQVLAELKEYATEVDVDFVQKAVRAIERCAIK<VEQSAERCVSTLLDLIQTKVNYVVQE-VIVV<HQIF

Parental  RKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAI
          RKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDN.DELLESFLEGFH.ES.QVQLTLLTAI
Retrocopy RKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNVDELLESFLEGFHNESAQVQLTLLTAI

Parental  VKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPT
          VKLFLKKPSETQELVQQVLSLATQDSDNPDL.DRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPT
Retrocopy VKLFLKKPSETQELVQQVLSLATQDSDNPDL*DRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPT

Parental  LLDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLL
          LLDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGT.TATNLEQPQVIPSQGDLL
Retrocopy LLDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTSTATNLEQPQVIPSQGDLL

Parental  GDLLNLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLG
          GDLLNLDLGPPVNVPQVSSM.MGAVDLLGGGLDSL.G
Retrocopy GDLLNLDLGPPVNVPQVSSMRMGAVDLLGGGLDSLVG

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_1925 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020316	1 retrocopy	retro_btau_1675,
Choloepus hoffmanni	ENSCHOG00000010864	1 retrocopy	retro_chof_2310,
Callithrix jacchus	ENSCJAG00000014853	1 retrocopy	retro_cjac_1850,
Gorilla gorilla	ENSGGOG00000015593	1 retrocopy	retro_ggor_3044,
Loxodonta africana	ENSLAFG00000015777	1 retrocopy	retro_lafr_446,
Myotis lucifugus	ENSMLUG00000002837	1 retrocopy	retro_mluc_2443,
Mustela putorius furo	ENSMPUG00000014910	1 retrocopy	retro_mputfur_704,
Mus musculus	ENSMUSG00000035152	1 retrocopy	retro_mmus_2503,
Nomascus leucogenys	ENSNLEG00000013939	2 retrocopies	retro_nleu_1925 , retro_nleu_2554,
Pongo abelii	ENSPPYG00000008188	1 retrocopy	retro_pabe_3793,
Pan troglodytes	ENSPTRG00000009021	1 retrocopy	retro_ptro_3248,
Rattus norvegicus	ENSRNOG00000009988	2 retrocopies	retro_rnor_1267, retro_rnor_574,