RetrogeneDB ID: retro_nleu_2668

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397393.1:2865351..2866467(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSNLEG00000012205
• Aliases: None
• Description: None

Sequence

>retro_nleu_2668
ATGTCTATGTGGGACTCCTTTAATCCGGAAAGTTACTAATTGACAAGAGCTTTCAGCTAACCAGATTCACTGAACTGAAG
GGCACAGGCTGCAAAGTGCCCCAAAATGTCCTGCAAAAATTGCTGGAATCTTTATAGGAGAACCACTTCCAAGAAGATGA
GCAGTTTCTGGTAGCCATTAATGCCAAGGCTTGGCATTAGAATTGATACTTGTGTCATTCCTTTGAAGCACGATGAACTT
TCCTTGGTTCAAACCATGGATTACATTTACTGATCATAGATGACCCTTACATGATGGGCAGGATGGCATGTGCCAATGTC
TTCAGTGACCTATATGCAATGGGGGTCACAGAATGTGACAATATGCTGATGCTCCTTGGAGTCAGTAATAAAATGACTGA
TAGGGAAAGGGATAAACTGATGCCTCTGATTATCCAGGGTTTTAAAAACGCAGCTGAGGAAGCAGGAAAGTCTGTAAGGA
GTGGCCAAACAGTATTAAACCCCTGGATTGTTCTGGGAGGAGTTGCTGCCAATGTCTGCCAGCCCAGTGAATTTATCATG
CCAGACAATGCAGTGCCAGGGGATGGGCTGGTGTTGACAAAACCCCTGGGGACACATGTGGCAGTGGTTGTGCACCAGTG
GCTGGATATTACTGGAAAACAGAATAAAATTAAATTAGTGGTCACCCAAGGACATGTAGAATTGGCCTACCAGGAGGTGA
TGATGAGCATGAGGATGCTCAACAGGACAACTGCAGGACTCATGCACACGTTCAATTCCCACGCAGGCACCGACATCACG
GGCTTTGGGATTTCGGGACTGGAGCAGAGCCTGGTCAAGTAGCAGAGGAACAAGGTGTCGTTTGTGATCCACAACATCCC
AGTGCTGGTCAAGATGGCTGCGGTGAGCAAAGCCTGCAGAAACATGTTCTGCCTCATGTACAGGACCTGCCAGGAGGCAT
CAGGAGGCCTTCTGATCTCCTTACCACATGAGCAAGCAGGTCGAGTCCATGCAGAGATGAAGTCCCCTAACTGTGGTGAA
GGCCACCAAGTATGAAATTATTGGGATTGAAGAGAAGGGCAAACACACAGCCAGAATCATAGACAAACCGTGGATC

Alignment

ORF - retro_nleu_2668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.05 %
• Parental protein coverage: 94.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSTRESFNPESYEL-DKSFRLTRFTELKGTGCKVPQDVLQKLLESLQENHFQEDEQFLGAV-MPRLGIGM
          MS...SFNPESY.L.DKSF.LTRFTELKGTGCKVPQ.VLQKLLESL.ENHFQEDEQFL.A..MPRLGI..
Retrocopy MSMWDSFNPESY*L<DKSFQLTRFTELKGTGCKVPQNVLQKLLESL*ENHFQEDEQFLVAI>MPRLGIRI

Parental  DTCVIPLRHGGLSLVQTTDYIY-PIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRER
          DTCVIPL.H..LSLVQT.DYIY..I.DDPYMMGR.ACANV.SDLYAMGVTECDNMLMLLGVSNKMTDRER
Retrocopy DTCVIPLKHDELSLVQTMDYIY<LIIDDPYMMGRMACANVFSDLYAMGVTECDNMLMLLGVSNKMTDRER

Parental  DKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQV
          DK.MPLIIQGFK.AAEEAG.SV..GQTVLNPWIVLGGVA..VCQP.EFIMPDNAVPGD.LVLTKPLGT.V
Retrocopy DKLMPLIIQGFKNAAEEAGKSVRSGQTVLNPWIVLGGVAANVCQPSEFIMPDNAVPGDGLVLTKPLGTHV

Parental  AVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQN
          AV.VHQWLDI..K.NKIKLVVTQ..VELAYQE.MM.M..LNRT.AGLMHTFN.HA.TDITGFGI.G..Q.
Retrocopy AVVVHQWLDITGKQNKIKLVVTQGHVELAYQEVMMSMRMLNRTTAGLMHTFNSHAGTDITGFGISGLEQS

Parental  LAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGE
          L.K.QRN.VSFVIHN.PVL.KMAAVSKAC.NMF.LM..TC.E.SGGLLI.LP.EQA.R..AE.KSP..GE
Retrocopy LVK*QRNKVSFVIHNIPVLVKMAAVSKACRNMFCLMYRTCQEASGGLLISLPHEQAGRVHAEMKSPNCGE

Parental  GHQA-WIIGIVEKGNRTARIIDKPRI
          GHQ...IIGI.EKG..TARIIDKP.I
Retrocopy GHQV>EIIGIEEKGKHTARIIDKPWI

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_2668 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.

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013555	1 retrocopy	retro_amel_21,
Canis familiaris	ENSCAFG00000004743	2 retrocopies	retro_cfam_1787, retro_cfam_250,
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Dipodomys ordii	ENSDORG00000014119	1 retrocopy	retro_dord_792,
Equus caballus	ENSECAG00000014281	1 retrocopy	retro_ecab_77,
Felis catus	ENSFCAG00000003921	1 retrocopy	retro_fcat_96,
Homo sapiens	ENSG00000086475	3 retrocopies	retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Gorilla gorilla	ENSGGOG00000003806	2 retrocopies	retro_ggor_147, retro_ggor_2924,
Loxodonta africana	ENSLAFG00000004670	1 retrocopy	retro_lafr_125,
Macropus eugenii	ENSMEUG00000012188	1 retrocopy	retro_meug_245,
Myotis lucifugus	ENSMLUG00000001971	2 retrocopies	retro_mluc_2350, retro_mluc_728,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Monodelphis domestica	ENSMODG00000016864	1 retrocopy	retro_mdom_86,
Mustela putorius furo	ENSMPUG00000000948	1 retrocopy	retro_mputfur_20,
Mus musculus	ENSMUSG00000026662	1 retrocopy	retro_mmus_248,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668 , retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Otolemur garnettii	ENSOGAG00000007807	1 retrocopy	retro_ogar_3026,
Ochotona princeps	ENSOPRG00000006587	3 retrocopies	retro_opri_271, retro_opri_655, retro_opri_670,
Procavia capensis	ENSPCAG00000015617	1 retrocopy	retro_pcap_341,
Pongo abelii	ENSPPYG00000002099	6 retrocopies	retro_pabe_1324, retro_pabe_1378, retro_pabe_2074, retro_pabe_2620, retro_pabe_3047, retro_pabe_3652,
Pan troglodytes	ENSPTRG00000002303	3 retrocopies	retro_ptro_1135, retro_ptro_1669, retro_ptro_3126,
Pteropus vampyrus	ENSPVAG00000002945	2 retrocopies	retro_pvam_115, retro_pvam_566,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,
Tursiops truncatus	ENSTTRG00000011114	1 retrocopy	retro_ttru_649,