RetrogeneDB ID: retro_nleu_2313

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397342.1:7187766..7188878(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTA2
• Ensembl ID: ENSNLEG00000012233
• Aliases: None
• Description: None

Sequence

>retro_nleu_2313
GAAGGAGAGATCGTGGCGCTGGTCATTGACAATGGTTCCGGCATGTGCAAAGCTCGCTTTCCTAGGAATGACGCCCCCAG
AGCTGTGTTTTCCTCCATCTTTGGGTGTCTCCGGCACTAGAGCATAATGGTGGGCATGGGCCAGGACTCCCACATGGGCG
ATGAGGCCCAGAGCAAGCAAGGCATCCTGACCCTGAAGTACCCCATCGAGCATGACATCATCACCAACTGGGACGACATG
GGGATCTGGCACCTCACCTTCTACAACAAGCTGCGCATGGCCCCAGAGGAGCACCCGGTGCTGTTGACCATGGCTCCCCT
GAACCCCAAGGCCAACAGAGAGAAGATGACTCATCATGTTCGAGATCTTCAATACTCGGGCCATATACATGGCCATCCAG
GCCGTGCTGTCCCTCTACACCTCTCGGCAAACCACTGGCATTGTCATGGACTCTGGGGACTGGGTCACACACACGGTGCC
CATCTACGAGGGCTATGCCCTCCCCCACACCATCCTGTGTCTGGACCTGGCTGGCCGGGACCTGACCCACTACCTCATGA
AGATTCTCACTGAGTGTGGCTACAGCTTCACCACCTTGGCCAAGTGGGAGATCGTGCGCAACGTCAAGGAGAAGCTGTGC
TACGTTGCCCTAGACTTCTAGCAGGAGATGGCCACCGCTGCATCCTCCTCTTCCCTGGAGAAGAGCTACGAGCTGTCCAA
TGGTCAGCTCATCACAATCTGCAATGAGTGGTTCCGGTGTCTGGAGGCACTGTTCCAGCCTTCCTTCCTGAGCATGGAAT
CTTGTGGCATCCATGAGACCACCATCAACTCCTTCATGAAGTACAAGGTGGACATCTGCAAAGACCTGTGCCAACACGGT
GCTGTCAGGCGGCACCACCATGTACCCGGGCATCGCCGACAGGATGCAGAAGGAGATCCCTGCCCTGGCACCCAGCACCA
TGAAGATCAAGATCATTGCACCCCCAGAGCACAAGTACTCGGTGTGGATTGGCGGCTCCATCCTGGCCTCACTGTCCACC
TTCCAGCAGATGTGGATTAGCAAGCAGGAGTACCACGAGTCGGGCCCCTCCATCGTCCACTGCAAATGCTTC

Alignment

ORF - retro_nleu_2313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEDSTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
          E....ALV.DNGSG.CKA.F...DAPRAVF.SI.G..RH...MVGMGQ.DS..GDEAQSK.GILTLKYPI
Retrocopy EGEIVALVIDNGSGMCKARFPRNDAPRAVFSSIFGCLRH*SIMVGMGQ-DSHMGDEAQSKQGILTLKYPI

Parental  EHGIITNWDDMEKIWHHSFYNELRVAPEEHPTLLTEAPLN-PKANREKMTQIMFETFNVPAMYVAIQAVL
          EH.IITNWDDM..IWH..FYN.LR.APEEHP.LLT.APLN.P....E....IMFE.FN..A.Y.AIQAVL
Retrocopy EHDIITNWDDMG-IWHLTFYNKLRMAPEEHPVLLTMAPLN>PRPT-ERR*LIMFEIFNTRAIYMAIQAVL

Parental  SLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVR
          SLY.S..TTGIV.DSGD.VTH.VPIYEGYALPH.I..LDLAGRDLT.YLMKILTE.GYSF.T.A..EIVR
Retrocopy SLYTSRQTTGIVMDSGDWVTHTVPIYEGYALPHTILCLDLAGRDLTHYLMKILTECGYSFTTLAKWEIVR

Parental  DIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYN
          ..KEKLCYVALDF..EMATAASSSSLEKSYEL..GQ.ITI.NE.FRC.E.LFQPSF..MES.GIHETT.N
Retrocopy NVKEKLCYVALDF*QEMATAASSSSLEKSYELSNGQLITICNEWFRCLEALFQPSFLSMESCGIHETTIN

Parental  SIMKCDIDIRKDLYANNVL-SGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASL
          S.MK...DI.KDL........G.T.MYPGIADRMQKEI.ALAPSTMKIKIIAPPE.KYSVWIGGSILASL
Retrocopy SFMKYKVDICKDLCQHGAV>GGTT-MYPGIADRMQKEIPALAPSTMKIKIIAPPEHKYSVWIGGSILASL

Parental  STFQQMWISKQEYDEAGPSIVHRKCF
          STFQQMWISKQEY.E.GPSIVH.KCF
Retrocopy STFQQMWISKQEYHESGPSIVHCKCF

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_2313 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 16 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313 ,
Nomascus leucogenys	ENSNLEG00000013385	15 retrocopies	retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys	ENSNLEG00000014347	1 retrocopy	retro_nleu_1585,
Nomascus leucogenys	ENSNLEG00000015157	1 retrocopy	retro_nleu_2751,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355, retro_vpac_651,