RetrogeneDB ID: retro_ggor_1896

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:161241849..161242686(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000022644
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: B3GAT3
• Ensembl ID: ENSGGOG00000013604
• Aliases: None
• Description: None

Sequence

>retro_ggor_1896
CTACGCGCTGGCCAGCCATGTCACTGCCTTCCTCCCCTGCTGGCAGCAGCTGAGCAGCTACGGCAGAAGGATCTGAGGAT
TTCCCAGCTGCAAGCGGAACTCCGACGGCCACCCCCTGCCCCTGCCCAGCCCCCTGAACCCGAGGCCCTGCCTACTATCT
ATGTTGTTACCCCCACCTATGCCAGGCTGGTACAGAAGGCAGAGTTGGTACGGCTGTCCCAGACACTGAGCCTGGTGCCC
CGGCTGCATTGACTGCTGGTGGAGGATGCTGAGGGTCCCACCCCGCTGGTCTCAGGGCTGCTGGCTGCCTCTGGCCGCCT
CTTCACACACCTGGTGGTCCTCACGCCCAAAGCCCAGCGACTTCGGGAGGGCAAGCCTGGCTGGGTTCATCCCCATGGTG
TCGAGCAGCGGAACAAGGTCCTGGACTGGCTCCGGGGCAGAGAGAGTGCTGTGGGTGGGGAGAAGGACCCATCACCACCA
GGGACCCAAGGAGTCGTGTACTTTGCTGACAGTGGCAACACCTACAGCTGGGAGCTGTTTGAGGAGATGCGCTGGACCCG
TGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGAGTCAAGGGCCCTCAGGTACAGGACAGCCGGGTAGTGG
GCTTCCACACAGCATGGGAGCCCAACAGGCCCTTCCCTGTGGATATGGCCGGATTTGCTGTGGCCCTGCCCTTGCTGTTA
GCTAAGCCCAATGCCCAGTTTGATTCCACTGCTCCCCGGAGCCACCTGGAGAGCAGTCTTCTAAGCCACCTTGTGGATCC
CAAGGACCTGGAGCCACGGGCTGCCAACTGCACTCGG

Alignment

ORF - retro_ggor_1896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 92.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQLGQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
          ...GQPC.CLPPL.AAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
Retrocopy LRAGQPCHCLPPLLAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV

Parental  RLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVEQRNKA
          RLSQTLSLVPRLH.LLVEDAEGPTPLVSGLLAASG.LFTHLVVLTPKAQRLREG.PGWVHP.GVEQRNK.
Retrocopy RLSQTLSLVPRLH*LLVEDAEGPTPLVSGLLAASGRLFTHLVVLTPKAQRLREGKPGWVHPHGVEQRNKV

Parental  LDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRAVSVWPVGLVGGLRFEGPQVQDG
          LDWLRGR..AVGGEKDP.PPGTQGVVYFAD..NTYS.ELFEEMRWTR.VSVWPVGLVGGLR..GPQVQD.
Retrocopy LDWLRGRESAVGGEKDPSPPGTQGVVYFADSGNTYSWELFEEMRWTRGVSVWPVGLVGGLRVKGPQVQDS

Parental  RVVGFHTAWEPNRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTR
          RVVGFHTAWEPNRPFPVDMAGFAVALPLLL.KPNAQFDSTAPR.HLESSLLSHLVDPKDLEPRAANCTR
Retrocopy RVVGFHTAWEPNRPFPVDMAGFAVALPLLLAKPNAQFDSTAPRSHLESSLLSHLVDPKDLEPRAANCTR

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	14.87 RPM
SRP007412_cerebellum	0.24 RPM	19.34 RPM
SRP007412_heart	0.09 RPM	3.10 RPM
SRP007412_kidney	0.04 RPM	5.40 RPM
SRP007412_liver	0.16 RPM	5.57 RPM
SRP007412_testis	0.41 RPM	4.66 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_1896 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1896 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2724
Pan troglodytes	retro_ptro_1841
Pongo abelii	retro_pabe_2266

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000149541	1 retrocopy	retro_hsap_2724,
Gorilla gorilla	ENSGGOG00000013604	1 retrocopy	retro_ggor_1896 ,
Nomascus leucogenys	ENSNLEG00000003956	1 retrocopy	retro_nleu_589,
Pongo abelii	ENSPPYG00000025907	1 retrocopy	retro_pabe_2266,
Pan troglodytes	ENSPTRG00000039665	1 retrocopy	retro_ptro_1841,