RetrogeneDB ID: retro_ggor_3068

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:149110784..149111752(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAB1
• Ensembl ID: ENSGGOG00000013842
• Aliases: None
• Description: None

Sequence

>retro_ggor_3068
GTGCAGAGCTTGGGACAGGGGAAGTCAGATGCGGTCGGGAGCCTAGCACTGCAGAGTGCTGGTGAGTCCAGACTCTGGCA
AGGCCACCATGCCACCAAGAGCGAGCACAGCCTCTCCCCAGCAGAACTGGGCTCCCACATGTCCCCAAAGGAGAGCAGCG
AGGCACTGGATGCTGCTGCTGTGCTCTCTGTGGCAGCGTGTGTGGAGCGGATGGCCCCCACACTGCCGAAAAGTGACTTG
AACGAAGTGAAAAAGCTGCTAAAAACCAACAAGAAGTTGGCCAAAATGCTTGGTCACATCTTTGAGATGAACGATAATGA
TCCACGCAAAGAGGAGGAAATTTGGAAATACAGTGAATATATGGCAGATTTGACTCAAAGAGGAAGGATGGAAAACATCT
CATGCTTCATGAGCTCACCGTTAATGAAGCGGCTGCTCAACTCTGTGTGAAGGATGATGCTCTGCTGACAGGAAGAGATG
AGCTTTTTGCCGTGGCGAGGCAGATTTCTCGAGAAGTCACCTATAAATATACTTACAGAACCACCAAGTCAAAATGTGAA
GAAAGAGATGAATTATCCTTGTAGAGGATTAAAGTGGAGGATGGGTTTCCAGATTTGCAGGATTCTGTGCAAACGCTCTT
CCAGCTGGCTAGAGCTAAGAGTGAAGAACTCGCAGCTCTTAGTTCACAGCAGCCTGAAAAGGTGATGGCAAAGCAGATGG
AGTTCGTCTGCAACCAAGCTGGCTATGAGAGACTGCAGCATGCCGAGAGGAGGCTGTCTGCAGGGCTTTACGGGGAGAGC
TCAGAAGAGCACAGTCCTAAAGGCTTGACTTCCGATAACTCAGATGGACAAGGAGAAACACCTTGGAATCTCCGAATGCC
TAATTTACAGAACAGACAACCCCATCATTTTGTGGTGGATGGGGAGCTGAGCAGACTTTATCCCAGTGAGGCAAAGCCCC
ACTCATCA

Alignment

ORF - retro_ggor_3068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.02 %
• Parental protein coverage: 70.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VQSLGQGKSDVIGSLALQSVGESRLWQGHHATESEHSLSPADLGSPASPKESSEALDAAAALSVAECVER
          VQSLGQGKSD..GSLALQS.GESRLWQGHHAT.SEHSLSPA.LGS..SPKESSEALDAAA.LSVA.CVER
Retrocopy VQSLGQGKSDAVGSLALQSAGESRLWQGHHATKSEHSLSPAELGSHMSPKESSEALDAAAVLSVAACVER

Parental  MAPTLPKSDLNEVKELLKTNKKLAKMIGHIFEMNDDDPHKEEEIRKYSA-IYGRFDSKRKDGKHLTLHED
          MAPTLPKSDLNEVK.LLKTNKKLAKM.GHIFEMND.DP.KEEEI.KYS..IYGRFDSKRKDGKHL.LHE.
Retrocopy MAPTLPKSDLNEVKKLLKTNKKLAKMLGHIFEMNDNDPRKEEEIWKYSE<IYGRFDSKRKDGKHLMLHE-

Parental  IQLTVNEAAAQLCVKDNALLTRRDELFALARQISREVTYKYTYRTTKSKCGERDELSPKRIKVEDGFPDF
          ..LTVNEAAAQLCVKD.ALLT.RDELFA.ARQISREVTYKYTYRTTKSKC.ERDELS..RIKVEDGFPD.
Retrocopy --LTVNEAAAQLCVKDDALLTGRDELFAVARQISREVTYKYTYRTTKSKCEERDELSL*RIKVEDGFPDL

Parental  QDSVQTLFQQARAKSEELAALSSQQPEKVMAKQMEFLCNQAGYERLQHAERRLSAGLYRQSSEEHSPNGL
          QDSVQTLFQ.ARAKSEELAALSSQQPEKVMAKQMEF.CNQAGYERLQHAERRLSAGLY..SSEEHSP.GL
Retrocopy QDSVQTLFQLARAKSEELAALSSQQPEKVMAKQMEFVCNQAGYERLQHAERRLSAGLYGESSEEHSPKGL

Parental  TSDNSDGQVGERPLNLRMPNLQNRQPHHFVVDGELSRLYPSEAKSHSS
          TSDNSDGQ.GE.P.NLRMPNLQNRQPHHFVVDGELSRLYPSEAK.HSS
Retrocopy TSDNSDGQ-GETPWNLRMPNLQNRQPHHFVVDGELSRLYPSEAKPHSS

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	0.48 RPM	15.78 RPM
SRP007412_cerebellum	0.32 RPM	16.04 RPM
SRP007412_heart	0.03 RPM	5.03 RPM
SRP007412_kidney	0.20 RPM	8.83 RPM
SRP007412_liver	0.21 RPM	9.68 RPM
SRP007412_testis	0.00 RPM	13.05 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_3068 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3068 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3822

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010241	1 retrocopy	retro_chof_2490,
Callithrix jacchus	ENSCJAG00000005748	1 retrocopy	retro_cjac_4224,
Gorilla gorilla	ENSGGOG00000013842	1 retrocopy	retro_ggor_3068 ,
Microcebus murinus	ENSMICG00000007306	2 retrocopies	retro_mmur_1155, retro_mmur_1211,
Nomascus leucogenys	ENSNLEG00000006665	1 retrocopy	retro_nleu_2288,
Pongo abelii	ENSPPYG00000013025	1 retrocopy	retro_pabe_3822,
Ictidomys tridecemlineatus	ENSSTOG00000000098	1 retrocopy	retro_itri_1621,
Tupaia belangeri	ENSTBEG00000011954	1 retrocopy	retro_tbel_3626,