RetrogeneDB ID: retro_nleu_1441

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397293.1:8468457..8469570(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK6
• Ensembl ID: ENSNLEG00000006476
• Aliases: None
• Description: None

Sequence

>retro_nleu_1441
GTAGACAATGACTGTGATAAAAGAGAATCCATCAAGACAATTCTCCTTACTGATCCCCAGAGTGTCAAAAATGCTCTACA
TGAAATCAAAATTATTAGAAGATTTGACACCATGACATTGTGAAAGTGTTTGAAATTCCTAGTACCAGTGGAAGCCAATT
AACAAACAATGTGAACTCTCTTACCAAACTCAACGGTATTTACACTTTTCAGAATTACATGGAGACAGACTTGGCTAATA
TGCTGGAGGAGGGCCCTTTACTGGAAAAGCATGCCAGACTTTTCGTGTATCAGCTGCTAAGGTGGCTTAAGTATATTCAC
TCTGCAAATGTATTGCAGAGATATCTCAAACCAGCTTATCTTTTCATTAATACTGAAGACACGATGCTGAAGATAGGGGA
CTTTTGTCTTGCAGAGATTATTGGATCCTCATTACTTCCATAAGGATCATCTTTCTGAAGGACTGGTAACTAAATGGTAC
AGATCGCCACATCTTTTACTTTCTCCTAATAGTTATAGTAAAGCCATTGACATGTGGGCTGCAGGCCACATCTTTGCCGA
AATGCTGACTGGTAAAACCCTTTTTGCAGGTGTACGTGAACTCAAACAGATGCAGCTGATTTTAGAATCTAGTCCTGTTA
TACATGACGAAGATTTTCAGGAGCTTCTCAGTGTAATTCCAGTTTACATTAGAAATGAAATGACTGAACCACAGCAACCT
TTAACTCAGCTGCTTCAGGGAATTAGTTGAGAAGCACTAGATCTCCTGGAACAAATTTTAACATTTATCTCTACAGATGG
GTTAACAGCAGAAGAAGCGCTCTCCCATCATTACATGAGCATATATTATTTTGCAATGGATGAGCAAATTTCAAGTCATC
TTTTTCATATTGAAGATGAAGTTTATGATATTTTGTTTATGGATGAAACTCACAGTCACATTTATAACTGGGAAAGGTAT
GATCGTTAGTTTTCAGCGCATGATTGGCCTATGTATAACAACTTTGATATTGATGAAGTTCTGCTTGACCCGAGAGCACT
GTCTGATGTCACTGATGAAGAAGAAAAACAAGTTGATCCCCAGAAATATTTGGATGGACATTGGGAAAAGTAT

Alignment

ORF - retro_nleu_1441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.41 %
• Parental protein coverage: 51.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLD-HDNIVKVFEILGPSGSQLTDDVGSLTELNSVYI
          VDNDCDKR..IK.I.LTDPQSVK.AL.EIKIIRR.D.H..IVKVFEI...SGSQLT..V.SLT.LN..Y.
Retrocopy VDNDCDKRESIKTILLTDPQSVKNALHEIKIIRRFD<HHDIVKVFEIPSTSGSQLTNNVNSLTKLNGIYT

Parental  VQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLA-
          .Q.YMETDLAN.LE.GPLLE.HARLF.YQLLR.LKYIHSANVL.R.LKPA.LFINTED..LKIGDF.LA.
Retrocopy FQNYMETDLANMLEEGPLLEKHARLFVYQLLRWLKYIHSANVLQRYLKPAYLFINTEDTMLKIGDFCLA>

Parental  RIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLIL
          R..DPHY.HK.HLSEGLVTKWYRSP.LLLSPN.Y.KAIDMWAAG.IFAEMLTGKTLFAG..EL.QMQLIL
Retrocopy RLLDPHYFHKDHLSEGLVTKWYRSPHLLLSPNSYSKAIDMWAAGHIFAEMLTGKTLFAGVRELKQMQLIL

Parental  ESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLEQILTFSPMDRLTAEEALSHPY
          ES.PV.H.ED.QELLSVIPVYIRN.MTEP..PLTQLL.GIS.EALD.LEQILTF...D.LTAEEALSH.Y
Retrocopy ESSPVIHDEDFQELLSVIPVYIRNEMTEPQQPLTQLLQGIS*EALDLLEQILTFISTDGLTAEEALSHHY

Parental  MSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSHIYNWERYHDCQFSEHDWPVHNNFDIDEVQLDPRAL
          MSIY.F.MDE.ISSH.FHIEDEV.DIL.MDETHSHIYNWERY.D..FS.HDWP..NNFDIDEV.LDPRAL
Retrocopy MSIYYFAMDEQISSHLFHIEDEVYDILFMDETHSHIYNWERY-DR*FSAHDWPMYNNFDIDEVLLDPRAL

Parental  SDVTDEEEVQVDPRKYLDGDREKY
          SDVTDEEE.QVDP.KYLDG..EKY
Retrocopy SDVTDEEEKQVDPQKYLDGHWEKY

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_1441 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000962	1 retrocopy	retro_cjac_2633,
Homo sapiens	ENSG00000069956	2 retrocopies	retro_hsap_1257, retro_hsap_2519,
Gorilla gorilla	ENSGGOG00000004003	1 retrocopy	retro_ggor_1571,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63,
Nomascus leucogenys	ENSNLEG00000006476	2 retrocopies	retro_nleu_1441 , retro_nleu_2095,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464, retro_ptro_2743, retro_ptro_3045,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445,
Tupaia belangeri	ENSTBEG00000007876	2 retrocopies	retro_tbel_1879, retro_tbel_2946,
Tursiops truncatus	ENSTTRG00000016253	2 retrocopies	retro_ttru_322, retro_ttru_75,