RetrogeneDB ID: retro_ggor_1470

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:21649822..21650137(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNJ2BP
• Ensembl ID: ENSGGOG00000014492
• Aliases: None
• Description: None

Sequence

>retro_ggor_1470
ATGTTTGCACCCGCAGTGATGCGTGCTTTGCACAAGAATAAGACTCTCCAGTACGAAGTCCCCATGTTGTTGCTAATTGT
TAGAGTTTCTTTTGGTGTTCGTGAGTTTTTACAAATCTGACATGATGCTGTGAAGATGAAAATTGATCCTGAGTTGGAAA
AAAACTGAAAGCAAATAGTATCATTAGAATCAGAATATGAGAAAATAAAAGACTCCACTTTTGATAACTGGAAGAATATC
CAAGGACCCAAGCCTTGGAAAGATCCTGACCTCCTCCAAGAAAGGAATCCAGAAACCCTTAAGACTAAGACAACT

Alignment

ORF - retro_ggor_1470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLAPAVMRAFRKNKTLRYGVPMLLLIVGGSFGLREFSQIRYDAVKSKMDPELEKKLKENKISLESEYEKI
          M.APAVMRA..KNKTL.Y.VPMLLLIV..SFG.REF.QI..DAVK.K.DPELEK..K....SLESEYEKI
Retrocopy MFAPAVMRALHKNKTLQYEVPMLLLIVRVSFGVREFLQI*HDAVKMKIDPELEKN*KQI-VSLESEYEKI

Parental  KDSKFDDWKNIRGPRPWEDPDLLQGRNPESLKTKTT
          KDS.FD.WKNI.GP.PW.DPDLLQ.RNPE.LKTKTT
Retrocopy KDSTFDNWKNIQGPKPWKDPDLLQERNPETLKTKTT

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	15.59 RPM
SRP007412_cerebellum	0.08 RPM	14.70 RPM
SRP007412_heart	0.00 RPM	14.17 RPM
SRP007412_kidney	0.00 RPM	37.45 RPM
SRP007412_liver	0.03 RPM	26.48 RPM
SRP007412_testis	0.10 RPM	32.12 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_1470 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1470 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2038
Pan troglodytes	retro_ptro_1355

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007586	1 retrocopy	retro_btau_1114,
Cavia porcellus	ENSCPOG00000023967	1 retrocopy	retro_cpor_836,
Gorilla gorilla	ENSGGOG00000014492	1 retrocopy	retro_ggor_1470 ,
Mus musculus	ENSMUSG00000090935	3 retrocopies	retro_mmus_1428, retro_mmus_1538, retro_mmus_1802,
Oryctolagus cuniculus	ENSOCUG00000008559	1 retrocopy	retro_ocun_885,