RetrogeneDB ID: retro_ggor_1414

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:58130926..58132012(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000023935
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDCCAG3
• Ensembl ID: ENSGGOG00000010905
• Aliases: None
• Description: None

Sequence

>retro_ggor_1414
GATTTGGGCTATGGAAAGGGGAAATGTTCTAAGCAGAGCCCGTCAGGAGCCCATGAGACACATTTTGGAGATGACAAATT
TGAAGATCTTGAAGAGGTAAATCCATTCTCCTTTAAAGAGTTTCTGAAGACCAAGAACCTCGGCCTGTCAAAAGAGGACC
CGGCCAGCAAAATTTATGCAAAGGAAGCGTCGAGGCATTCACTGGGACTTGACCACAACTCCCCACTCTCCCAAACCGGG
GGGTATGGCCTGGAGTATCAGCAGCCATTTTTCGAGGACCCGACAGGGGCCGGTGACCTCCTGGATGAGGAGGAGGATGA
GGACACCGGATGGAGTAGGGCCTACCTGCCGTCCGCCATCCAGCAGACTCACCCAGAGAGGGTCCCTGCCTGCACGTCGC
CCTGCAGCACATACCTTTCCTTTTTCTCCACCCCGTCAGAGCTGGCAGGGCCCGAGTCTCTGCTCCCGTGGGCGTTGAGT
GACACTGATTCTCGCGTGTCTCCGGCCTCTCCGGCAGGGAGTCCTAGCACAGATTTTGCGGCTCATGGAGAGTCTCTGGG
AGACAGGCACCTGCGGACGCTGCAGATAAGTTACGAAGCACTGAAAGATGAAAATTCTAAGCTGAGAAGAAAGCTGAATG
AGGTTCAGAGCTTCTCTGAAGCTCAAACAGAAATGGTGAGGACACTTGTGCAGAAATTAGAAGCAAAAATGATCAACGAG
GAAAGCGACTACCACGACTTGGAGTTGGTGGTTCAGCAGGTGGAGCAGAACCTGGAGCTGATGACCAAACGGGCTGTAAA
GGCAGAAAACCATGTCGTGAAACTGAAACAGGAAATCAGTTTGCTGCAGGCGCAGGTCTCCAGCTTCCAGCGAGAGAATG
AAGCCCTGCGGTGCGACCAGGGGGCCAGCCTGACAGTGGTGAAGCAGAACGCCGACGTGGCCTTGCAGAACCTCTGGGTG
GTCATGAACAGCGCACAGGCTTCCGTTAAGCAACTGGTTTCCGGAGCTGAGACACTGAATCTTGCTGCCGAAATCCTTAA
ATCTATAGACAGAATTTCTGAAATTAAAGACGAGGAGGAAGACTCT

Alignment

ORF - retro_ggor_1414 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.27 %
• Parental protein coverage: 87.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFGYGKGKCSKQSPSGAHGTHFGDDRFEDLEEANPFSFKEFLKTKNLGLSKDDPASRIYAKEASRHSLGL
          D.GYGKGKCSKQSPSGAH.THFGDD.FEDLEE.NPFSFKEFLKTKNLGLSK.DPAS.IYAKEASRHSLGL
Retrocopy DLGYGKGKCSKQSPSGAHETHFGDDKFEDLEEVNPFSFKEFLKTKNLGLSKEDPASKIYAKEASRHSLGL

Parental  DHNSPPSQTGGYGLEYQQPFFEDPTGASDLLDEEEDEDIRWSGAYLPSAIEQTHPERVPAGTSPCSTYLS
          DHNSP.SQTGGYGLEYQQPFFEDPTGA.DLLDEEEDED..WS.AYLPSAI.QTHPERVPA.TSPCSTYLS
Retrocopy DHNSPLSQTGGYGLEYQQPFFEDPTGAGDLLDEEEDEDTGWSRAYLPSAIQQTHPERVPACTSPCSTYLS

Parental  FFSTPSELAGPESLPSWALSDTDSRVSPASPAGSPSADFAAHGESLGDRHLRTLQISYDALKDENSKLRR
          FFSTPSELAGPESL..WALSDTDSRVSPASPAGSPS.DFAAHGESLGDRHLRTLQISY.ALKDENSKLRR
Retrocopy FFSTPSELAGPESLLPWALSDTDSRVSPASPAGSPSTDFAAHGESLGDRHLRTLQISYEALKDENSKLRR

Parental  KLNEVQSFSEAQTEMVRTLERKLEAKMIKEESDYHDLESVVQQVEQNLELMTKRAVKAENHIVKLKQEIS
          KLNEVQSFSEAQTEMVRTL..KLEAKMI.EESDYHDLE.VVQQVEQNLELMTKRAVKAENH.VKLKQEIS
Retrocopy KLNEVQSFSEAQTEMVRTLVQKLEAKMINEESDYHDLELVVQQVEQNLELMTKRAVKAENHVVKLKQEIS

Parental  LLQAQVSNFQRENEALRCGQGASLTVAKQNADVALQNLRVVMNSAQASIKQLVSGAETLNLVAEILKSID
          LLQAQVS.FQRENEALRC.QGASLTV.KQNADVALQNL.VVMNSAQAS.KQLVSGAETLNL.AEILKSID
Retrocopy LLQAQVSSFQRENEALRCDQGASLTVVKQNADVALQNLWVVMNSAQASVKQLVSGAETLNLAAEILKSID

Parental  RISEIKDEEEDS
          RISEIKDEEEDS
Retrocopy RISEIKDEEEDS

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	0.00 RPM	9.69 RPM
SRP007412_cerebellum	0.00 RPM	9.69 RPM
SRP007412_heart	0.00 RPM	5.22 RPM
SRP007412_kidney	0.04 RPM	25.35 RPM
SRP007412_liver	0.08 RPM	18.83 RPM
SRP007412_testis	0.10 RPM	47.55 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_1414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1414 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1944
Pan troglodytes	retro_ptro_1300

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000165689	1 retrocopy	retro_hsap_1944,
Gorilla gorilla	ENSGGOG00000010905	1 retrocopy	retro_ggor_1414 ,
Mus musculus	ENSMUSG00000026927	3 retrocopies	retro_mmus_1545, retro_mmus_3492, retro_mmus_711,
Nomascus leucogenys	ENSNLEG00000008186	1 retrocopy	retro_nleu_891,
Otolemur garnettii	ENSOGAG00000015872	1 retrocopy	retro_ogar_3418,
Pongo abelii	ENSPPYG00000019772	2 retrocopies	retro_pabe_1612, retro_pabe_256,
Pan troglodytes	ENSPTRG00000021555	1 retrocopy	retro_ptro_1300,
Rattus norvegicus	ENSRNOG00000018876	2 retrocopies	retro_rnor_1215, retro_rnor_2770,