RetrogeneDB ID: retro_ggor_752

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 11:117771411..117772340(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX39B
• Ensembl ID: ENSGGOG00000005989
• Aliases: None
• Description: None

Sequence

>retro_ggor_752
CTTCTGCTTCTCCACTCTGGGGAACAGGCGCTGTTGGCTTCCCAAGCCATGGTCGGTTCTCTAAATATATGCCCAATGTC
AAGTTTGCTGTATTTTTTGGTGGTCTATCAAGAAGGATGAAGAGGTGCTGAAGAAGAACTGCCTGCATATCGTGGTGGGG
ACTCCAGGCTGTATCCTAGGCCTGGCTGGAAATAAAAGCCTCAACCTCAAACACATAAAACACTTTATTTCAAATGAATG
TGATAAGACGTTTGAACAGCTCAACATGTGTCGGGATGTCCAGGGAATTTTTCGCATGACCCCACCGTGAGAAGCCGGTC
ATGATGTTCAGGGCTACCTTGAGCAAAGAGATCCGTCCAGTCTGCCACAAGTTCATGCAAGATCCAGTGGAGATCTTCGT
GGATAATGAGACGAAGTTGATGCTGCATGGGTTGCAGCAGTATTACATGAAACTGAAGGACAACCAGAAGAACTGGAAGC
GCTATGACCTTCTGAATGTCCTTGAGTTCAACCAGGTGATGATCTTTTTGAAGTCTGTGCAGCAGCGCATTGCCTCAGCC
CAGCTACTGGGTGGAGCAGAACTTCCCAGCCATTGCCATCCACCGCGGGATGCCCCAGGGCAGAGGCTGTCTCAGTATCA
GCAGTTTAAAGATTTTCAATGGTGAATTCTTGTGGCTACCAACCTATTTGGCCAAGGAATGGACATTGAGCGGGTGAACA
TTGCTTTTAATTATGACATGCCTGAGGATTCTGACACCTACCTGCATTGGGTGGCCAGAGCCAGCGGGTTTGGCACCAAG
GGCTTGGCTATCACATTTGTGTCTGACAAGAATGATGCCAAGATCCTCAATGACATGCAGGATCGCTTTGAGGTCAATCG
TAGTGATCTGCCTGATGAGAGAGACATCTTCTCCTGCTTTGAAAAGACA

Alignment

ORF - retro_ggor_752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.85 %
• Parental protein coverage: 70.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LVMCHTRELAFQISK-EYERFSKYMPNVKVAVFFGGLS-IKKDEEVLKKNCPHIVVGTPGRILALARNKS
          L...H..E.A...S.....RFSKYMPNVK.AVFFGGLS..K..E.VLKKNC.HIVVGTPG.IL.LA.NKS
Retrocopy LLLLHSGEQALLASQ<SHGRFSKYMPNVKFAVFFGGLS<KKDEE-VLKKNCLHIVVGTPGCILGLAGNKS

Parental  LNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTP-HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDD
          LNLKHIKHFI..ECDK..EQL.M.RDVQ.IFRMTP..EK.VMMF.ATLSKEIRPVC.KFMQDP.EIFVD.
Retrocopy LNLKHIKHFISNECDKTFEQLNMCRDVQGIFRMTP>REKPVMMFRATLSKEIRPVCHKFMQDPVEIFVDN

Parental  ETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLL-VEQNFPAIAIHRGMP
          ETKL.LHGLQQYY.KLKDN.KN.K..DLL.VLEFNQV.IF.KSVQ..IA.AQLL.VEQNFPAIAIHRGMP
Retrocopy ETKLMLHGLQQYYMKLKDNQKNWKRYDLLNVLEFNQVMIFLKSVQQRIASAQLL>VEQNFPAIAIHRGMP

Parental  Q-EERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFV
          Q...RLS.YQQFKDFQ..ILVATNLFG.GMDIERVNIAFNYDMPEDSDTYLH.VARA..FGTKGLAITFV
Retrocopy Q<GQRLSQYQQFKDFQW*ILVATNLFGQGMDIERVNIAFNYDMPEDSDTYLHWVARASGFGTKGLAITFV

Parental  SDENDAKILNDVQDRFEVNISELPDEIDISSYIEQT
          SD.NDAKILND.QDRFEVN.S.LPDE.DI.S..E.T
Retrocopy SDKNDAKILNDMQDRFEVNRSDLPDERDIFSCFEKT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.10 RPM	99.12 RPM
SRP007412_cerebellum	0.08 RPM	186.51 RPM
SRP007412_heart	0.00 RPM	56.29 RPM
SRP007412_kidney	0.08 RPM	141.03 RPM
SRP007412_liver	0.00 RPM	97.26 RPM
SRP007412_testis	0.00 RPM	111.16 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_752 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_752 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_804
Macaca mulatta	retro_mmul_1126

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000005989	1 retrocopy	retro_ggor_752 ,
Macropus eugenii	ENSMEUG00000008264	2 retrocopies	retro_meug_1623, retro_meug_288,