RetrogeneDB ID: retro_nleu_11

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397271.1:22264778..22266164(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018619
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EEF1A2
• Ensembl ID: ENSNLEG00000010060
• Aliases: None
• Description: Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:G1RGC3]

Sequence

>retro_nleu_11
ATGGGAAAGGAAAAGACTCATATCAACATTGTCGGCATTGGACATGTAGATTCGGGCAAGTCCACCACTACTGGCCATCT
GATCTATAAATGCGGTGGCATTGACAAAAGAACCATTGAAAAATTTGAGAAGGAGGCTGCTGAGATGGGAAAGGGCTCCT
TCAAGTATGCCTGGGTCTTGGATAAACTGAAAGCTGAGTGTAAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTT
GAGACCAGCAAGTACTATGTGACCATCACTGATGCCCCAGGACACAGAGACTTCATCAAAAACATGATTACAGGGACATC
TCAGGCTGACTGTGCTGTCGTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGTATCTCCAAGAATGGGCAGACCC
GAGAGCGTGCCCTTCTGCCTTACACACTGGGTGTGAAACAATTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCA
CCCTACAGCCAGAAGAGATACGAGGAAATTGTTAAGGAAGTCACCACTTACAGTAAGAAAATTGGCTACAACCCCGACAC
AGTAGCATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGCTGGAGCCAAGTGCTAACATGCCTTGGTTCAAGGGAT
GGAAAGTCACCCGTAAGGATTGCAATGCCAGTGAAGCCACACTGCTTGAGACTCTGGACTGCATCCTACCACCAACTCGT
CCAACTGACAAGCCCTTGCACCTGCCTCTCCAGGATGTCTACAAAATTGGTGGTATTGGTACTGTTCCTGTTGGCCGAGT
AGAGACTGGTGTTCTCAAACCTGGTATGGTGGTCACCTTTGCTCCAGTCAACGTTACAACGGAAGTAAAATCTGTCAAAA
TGCACCATGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAATGTGGGCTTCAATGTCAAGAATGTGTCTGTCAAGGATGTT
CATCGTGGCAACGTTGCTGGTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGGCTTCACTGCTCAGGTGATTATCCT
GAACCATCCAGGGCAAATAAGCACTGGCTATGCCCCTGTATTGGATTGCCACACGGCTCACATTGCATGCAAGTTTGCTG
AGCTGAAAGAAAAGATTGATCGTCGTTCTGGTAAAAAGCTGGAAGATGGCCCTAGATTCTTGAAGTCTGGTGATGCTGCC
ATTGTTGATATGGTTCCTGGCAAGCCCACGTGTGTTGAGAGCTTCTCAGACTATCCACCTTTGGGTCGTTTCGCTGTTCG
TGATATGAGACAGACAGTTGCGGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCTGCTGGAGCTGGCAAGGTCACCAAGT
CTGCCCAGAAAGCTCAGAAGGCTAAA

Alignment

ORF - retro_nleu_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
          MGKEKTHINIV.IGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAE..RG
Retrocopy MGKEKTHINIVGIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAECKRG

Parental  ITIDISLWKFETTKYYITIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
          ITIDI.LWKFET.KYY.TI.DAPGHRDFIKNMITGTSQADCAV.IVAAGVGEFEAGISKNGQTRE.ALL.
Retrocopy ITIDIALWKFETSKYYVTITDAPGHRDFIKNMITGTSQADCAVVIVAAGVGEFEAGISKNGQTRERALLP

Parental  YTLGVKQLIVGVNKMDSTEPAYSEKRYDEIVKEVSAYIKKIGYNPATVPFVPISGWHGDNMLEPSPNMPW
          YTLGVKQLIVGVNKMDSTEP.YS.KRY.EIVKEV..Y.KKIGYNP.TV.FVPISGW.GDNMLEPS.NMPW
Retrocopy YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVTTYSKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW

Parental  FKGWKVERKEGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGILRPGMVVTF
          FKGWKV.RK..NAS...LLE.LD.ILPPTRPTDKPL.LPLQDVYKIGGIGTVPVGRVETG.L.PGMVVTF
Retrocopy FKGWKVTRKDCNASEATLLETLDCILPPTRPTDKPLHLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF

Parental  APVNITTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDIRRGNVCGDSKSDPPQEAAQFTSQVIILNHP
          APVN.TTEVKSV.MHHEALSEALPGDNVGFNVKNVSVKD..RGNV.GDSK.DPP.EAA.FT.QVIILNHP
Retrocopy APVNVTTEVKSVKMHHEALSEALPGDNVGFNVKNVSVKDVHRGNVAGDSKNDPPMEAAGFTAQVIILNHP

Parental  GQISAGYSPVIDCHTAHIACKFAELKEKIDRRSGKKLEDNPKSLKSGDAAIVEMVPGKPMCVESFSQYPP
          GQIS.GY.PV.DCHTAHIACKFAELKEKIDRRSGKKLED.P..LKSGDAAIV.MVPGKP.CVESFS.YPP
Retrocopy GQISTGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPRFLKSGDAAIVDMVPGKPTCVESFSDYPP

Parental  LGRFAVRDMRQTVAVGVIKNVEKKSGGAGKVTKSAQKAQKA
          LGRFAVRDMRQTVAVGVIK.V.KK..GAGKVTKSAQKAQKA
Retrocopy LGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKA

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_11 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 14 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Latimeria chalumnae	ENSLACG00000002952	1 retrocopy	retro_lcha_39,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Macropus eugenii	ENSMEUG00000005018	23 retrocopies	retro_meug_1067, retro_meug_110, retro_meug_1160, retro_meug_1240, retro_meug_1334, retro_meug_135, retro_meug_1421, retro_meug_1451, retro_meug_1465, retro_meug_1501, retro_meug_1662, retro_meug_1690, retro_meug_1710, retro_meug_1829, retro_meug_2023, retro_meug_2044, retro_meug_2050, retro_meug_316, retro_meug_601, retro_meug_755, retro_meug_792, retro_meug_850, retro_meug_920,
Myotis lucifugus	ENSMLUG00000016760	1 retrocopy	retro_mluc_1250,
Mustela putorius furo	ENSMPUG00000008289	3 retrocopies	retro_mputfur_1030, retro_mputfur_609, retro_mputfur_761,
Nomascus leucogenys	ENSNLEG00000001476	6 retrocopies	retro_nleu_1492, retro_nleu_1584, retro_nleu_1754, retro_nleu_1901, retro_nleu_235, retro_nleu_829,
Nomascus leucogenys	ENSNLEG00000010060	2 retrocopies	retro_nleu_11 , retro_nleu_1489,
Ornithorhynchus anatinus	ENSOANG00000004908	1 retrocopy	retro_oana_73,
Otolemur garnettii	ENSOGAG00000004630	8 retrocopies	retro_ogar_1067, retro_ogar_2034, retro_ogar_2329, retro_ogar_2497, retro_ogar_2583, retro_ogar_3191, retro_ogar_3270, retro_ogar_643,
Ictidomys tridecemlineatus	ENSSTOG00000028862	1 retrocopy	retro_itri_1028,
Tursiops truncatus	ENSTTRG00000001835	1 retrocopy	retro_ttru_993,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,