RetrogeneDB ID: retro_nleu_2157

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397332.1:7238958..7241024(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM35A
• Ensembl ID: ENSNLEG00000011652
• Aliases: None
• Description: family with sequence similarity 35, member A [Source:HGNC Symbol;Acc:28773]

Sequence

>retro_nleu_2157
GTTTCTGAAACACAGAATATAGAATCCCAGAAGATTCACTCCTCTAGACCGAGTGATATAACTAGCTCTAATATGCAAAT
ATGTGGATTTAAAAGCACAGTTCCTCATTTAACCAAAGAAGAAAAGTATCAAAACTTCTCAGTGAAAATAAAATTATAGA
TGAACAGCCTAAACATCAGTCAGATATGTGTGGTCAGAACTTTAACACAAATTTGTTTCAGTTAGGCCATAAATGTGCAG
CTATGTTGGATTTGGTTTGTAGTACTGAACAAATTAATATAGGACCTGAAGTGGTACAAAGAGAGTGTGTGCCAACGGAA
TATCATGAAATACAAAACCAGTGTTTGGGATTATTTTCCTCGAACGCAGTAGATAAGTCAAGGTCCGAAGCAGCAGTTAG
GAAGGTCTCAGACCTTAAAATATCAACTGATACAGAATTTCTCAGTATAATTACCTCCAGCTAGGTTGCTGTTTTAGCTC
AAAAGAAAGATAAAAGGCGGAGTCCTATAAATAAAGGGAATGTAAACATGGAGACTGAACCAAAGGCAAGTTACGGGGAG
GTAAGAATACCTGAAGAGTATTGGATTCAGCTTGATGGTTTTACAGAAACATATGAAAGTGGACAAAACCAAGCATATTC
CCTTGAACTTTTTAGTCCTGTTTGTCCTAAAACAGAAAATAGCCGCATTCACATAAACTCTGATAAAGGTCTTGAAGAAC
ATACGGGATCTCAAGAACTTTTCAGTTCTGAAGATGAACTGCCACCAAATGAGATACGTATTGAGTTGTGTAGCTCAGGA
ATACTGGGTTCCCAACTAAATGCCTTCCACAAAAGTGCTATTAAAAGAAGCTGCACCTCTGAAGATAAAGTGGGCCAGTC
TGAAGCTCTATCTAGAGTCCTTCAAGTAGCTAAGAAAATGAAGTTGATTTCTAATGGAGGAGATTCTGCTGTAGAAATGG
ATCGGAGGAATGTGTCTGAATTTAAGGGTATTAAAAAAATATCATTAATAAAAAAACTGTGATTCTAAAAGCCAGAAGTA
TAATTGTTTACTCATGGTGCTATCTCCATGCCATGTGAAGGAAATAAACATAAAATTCAGGCCAAATTCTGGCTCTAAAG
TGCCTTTAGCAACAGTTACAGTAATTGATCAATCAAAAACTAAGAAGAAGGTTTTTCTGCGGAGGACTGCAGCATTTTGG
GCATTTACAGTGTTTCTTGGAGATATAATTTTACTCACAGATGTTGTATTCATGAGGACCAATGGGTTGGCAAGACAGTA
CTACAATCAACATTTAGCAGTCAGTTATTAAATCTTGGGAGTTATTCATCTATTCAGCCTGAAGAATATTCCAGTATAGT
TAGTGACGTTGTACTTCAAGACTTTCTGGCATATATGTCCTCAAAACATTCCTACCTCAGAGATCTTCCTCCGAGGCAGC
CTCAGAGGGTGAACAGTATCGACTTTGTAGAATTGGAGCACCTTCAACCTGATGTATTAGTCCATGCAGTACTAAGAGTT
GTTGATTTCACTATACTGACAGAGGCAGTATACAGTTATAGAGGACAGAAGCAGAAAAAAGTTATGTTAACAGTGGAACA
GGCCCAAGATCAACATTATGTGCTTGTATTATGGGGTCCTGGAGCAGCCTGGTACCCTCAACTTCAAAGGAAAAAAGGTT
ATATTTGGGAATTTAAATATCTTTTTGTTCAGCACACTTACACACTAGAAAACCTAGAATTGCATACGGTGCCTTGGTCA
TCCTGTGAGTGCTTGTTTGATGATGATATAACGGCAATTACATTTAAAGCAAAATTTCAAAAAAATGCACCCTCCTTTGT
GAAGATATCAGACTTAGCAACCCGCCTAGAGGATAAATGTTCAGGAGTCGTTCTAATTAAAGCCCAGATTTCAGAGCTGG
CATTTCCTATTACAGCAGCTCAGAAGATAGCTCTAAATGCTCACAGTTCTCTGAAGAGTATTTTTTCTTCTCTTCCCAAC
ATCGTATATACTGGCTATGCAAAATGTGGATTGGAACTAGAAACAGATGAGAACAGGATCTACAAA

Alignment

ORF - retro_nleu_2157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.64 %
• Parental protein coverage: 76.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VSETQNIESQKIHSSRLSDITSSNMQICGFKSTVPHLAKEEKDQ-KLLSENKIIDEQPKHQADICGQNFN
          VSETQNIESQKIHSSR.SDITSSNMQICGFKSTVPHL.KEEK.Q.KLLSENKIIDEQPKHQ.D.CGQNFN
Retrocopy VSETQNIESQKIHSSRPSDITSSNMQICGFKSTVPHLTKEEKYQ<KLLSENKIIDEQPKHQSDMCGQNFN

Parental  TDLFQLGHKCAAILDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVDNSRSEAAVRKVSDL
          T.LFQLGHKCAA.LDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVD.SRSEAAVRKVSDL
Retrocopy TNLFQLGHKCAAMLDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVDKSRSEAAVRKVSDL

Parental  KISTDTEFLSIITSSQVAFLAQKKDKGRSPINKGNVNMEAEPKASYGEIRIPDENSIQLDGFTEAYESGQ
          KISTDTEFLSIITSS.VA.LAQKKDK.RSPINKGNVNME.EPKASYGE.RIP.E..IQLDGFTE.YESGQ
Retrocopy KISTDTEFLSIITSS*VAVLAQKKDKRRSPINKGNVNMETEPKASYGEVRIPEEYWIQLDGFTETYESGQ

Parental  NQAYSLELFSPVCPKTENSCIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGILCSQLNTFHKS
          NQAYSLELFSPVCPKTENS.IHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGIL.SQLN.FHKS
Retrocopy NQAYSLELFSPVCPKTENSRIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGILGSQLNAFHKS

Parental  AIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKKTSLI-KNCDSKSQKYN
          AIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKK.SLI.KNCDSKSQKYN
Retrocopy AIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKKISLI>KNCDSKSQKYN

Parental  CLVMVLSPCHVKEINIKCGRNSGSKVPLATVTVIDESETKKKVFLWRTAAFWAFTVFLGDIILLTDVV-I
          CL.MVLSPCHVKEINIK...NSGSKVPLATVTVID.S.TKKKVFL.RTAAFWAFTVFLGDIILLTDVV.I
Retrocopy CLLMVLSPCHVKEINIKFRPNSGSKVPLATVTVIDQSKTKKKVFLRRTAAFWAFTVFLGDIILLTDVV<I

Parental  HEDQWVGETVLQSTFSTQLLNLGSYSSIQPEECSSVVSDVVLQDLLAYVSSKHSYLRDLPPRQPQRVNSI
          HEDQWVG.TVLQSTFS.QLLNLGSYSSIQPEE.SS.VSDVVLQD.LAY.SSKHSYLRDLPPRQPQRVNSI
Retrocopy HEDQWVGKTVLQSTFSSQLLNLGSYSSIQPEEYSSIVSDVVLQDFLAYMSSKHSYLRDLPPRQPQRVNSI

Parental  DFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQR
          DFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQR
Retrocopy DFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQR

Parental  KKGYIWEFKYLFVQRSYTLENLELHTTPWSSCECLFDDDIRAITFKAKFQKSAPSFVKISDLATHLEDKC
          KKGYIWEFKYLFVQ..YTLENLELHT.PWSSCECLFDDDI.AITFKAKFQK.APSFVKISDLAT.LEDKC
Retrocopy KKGYIWEFKYLFVQHTYTLENLELHTVPWSSCECLFDDDITAITFKAKFQKNAPSFVKISDLATRLEDKC

Parental  SGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTGCAKCGLELETDENRIYK
          SGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTG.AKCGLELETDENRIYK
Retrocopy SGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTGYAKCGLELETDENRIYK

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_2157 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000017	1 retrocopy	retro_dnov_2237,
Homo sapiens	ENSG00000122376	1 retrocopy	retro_hsap_1370,
Nomascus leucogenys	ENSNLEG00000011652	3 retrocopies	retro_nleu_1073, retro_nleu_2157 , retro_nleu_840,
Pongo abelii	ENSPPYG00000002828	1 retrocopy	retro_pabe_1137,
Pan troglodytes	ENSPTRG00000002465	1 retrocopy	retro_ptro_941,