RetrogeneDB ID: retro_ggor_2341

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:53695868..53696767(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A20
• Ensembl ID: ENSGGOG00000028046
• Aliases: None
• Description: None

Sequence

>retro_ggor_2341
ATAGCCGACCAGCCAAAGCCCATCAGCCTGCTCAAGAACCTGCTGGCCAGTGGCTTTGGTGGCATGTGCCTGGTGTTCAT
GGGGCACCCTCTGGACACTGTCAAGGTCCGACTGCAGACACAGCCACTGAGTTTGCCTAGACAGCCTCCCATGTACTCTG
GGACCTTTGACTCTCTCCCAAAGACTCTTAGAAGGGACATCACAGGGCTATATAAGGGAATGGCTGCCCCTATCATCGGT
GTCACCCCCATGTTTGCTGTGTGCTTCTTTGGGTTTGGTTTGAGGAAGAAACTATGACAGAAACACCCAGAAGATGTGCT
CAGCTATCCCCAGCTGTTTGCAGCTGGGATGTTATCTGGTACATTCACCACAGGCATCGTGACCCCTGGAGAACCCATCA
AGTCCTTGTTACACTTTCAGCCTTCTTCAGGGGAAACCAAGTACACTGGAACCTTGGACTGTGCAAAAAGTTGTACCAGG
AGTTTCAGATCCGAGGCATCTACAAAGGGACCATGCTTACCCTTATGTGAGATGTTCCAGCTAGCAGAACGTATTTCATG
ACAAATGAATGGCTAAAAAATGTCTTCACTCCGGAACGAAAGAGGGTCTGTGAGTTCAGTGTGCCTTGAATCCTGGCAGC
TGGGTGCATTGCAGGGATCTTCAACTGGGCAATGGCAGTCCCGCAAGATGTGCTCAAGTCTCCCTTCCAGACTGCACCTC
CTGGGAAATATCCTAACGGTTTTGGAGATGTGCTGAGGGAGCTGATCTGGGATGAAGGAATCACATCCTTGTCTAAAGGG
TCTGATGCAGTGATGACCCGAGCCTTCCCAGCCAATGCAGCCTGTTTCCTTGGCCTTGAAGTTGCCATGAAGTTTCTTAA
TTGGGCCACCCCCAACTTG

Alignment

ORF - retro_ggor_2341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADQPKPISPLKNLLAGGFGGVCLVFVGHPLDTVKVRLQTQPPSLPGQPPVYSGTFDCFRKTLFREGITG
          .ADQPKPIS.LKNLLA.GFGG.CLVF.GHPLDTVKVRLQTQP.SLP.QPP.YSGTFD...KTL.R..ITG
Retrocopy IADQPKPISLLKNLLASGFGGMCLVFMGHPLDTVKVRLQTQPLSLPRQPPMYSGTFDSLPKTLRRD-ITG

Parental  LYRGMAAPIIGVTPMFAVCFFGFGLGKKLQQKHPEDVLSYPQLFAAGMLSGIFTTGIMTPGERIKCLLQI
          LY.GMAAPIIGVTPMFAVCFFGFGL.KKL.QKHPEDVLSYPQLFAAGMLSG.FTTGI.TPGE.IK.LL..
Retrocopy LYKGMAAPIIGVTPMFAVCFFGFGLRKKL*QKHPEDVLSYPQLFAAGMLSGTFTTGIVTPGEPIKSLLHF

Parental  QASSGESKYTGTLDCAK-KLYQEFGIRGIYKGTVLTLMRDVPASGMYFMTYEWLKNIFTPEGKRVSELSA
          Q.SSGE.KYTGTLDCAK.KLYQEF.IRGIYKGT.LTLM.DVPAS..YFMT.EWLKN.FTPE.KRV.E.S.
Retrocopy QPSSGETKYTGTLDCAK<KLYQEFQIRGIYKGTMLTLM*DVPASRTYFMTNEWLKNVFTPERKRVCEFSV

Parental  PRILVAGGIAGIFNWAVAIPPDVLKSRFQTAPPGKYPNGFRDVLRELIRDEGVTSLYKGFNAVMIRAFPA
          P.IL.AG.IAGIFNWA.A.P.DVLKS.FQTAPPGKYPNGF.DVLRELI.DEG.TSL.KG..AVM.RAFPA
Retrocopy P*ILAAGCIAGIFNWAMAVPQDVLKSPFQTAPPGKYPNGFGDVLRELIWDEGITSLSKGSDAVMTRAFPA

Parental  NAACFLGFEVAMKFLNWATPNL
          NAACFLG.EVAMKFLNWATPNL
Retrocopy NAACFLGLEVAMKFLNWATPNL

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	11.37 RPM
SRP007412_cerebellum	0.00 RPM	8.51 RPM
SRP007412_heart	0.00 RPM	16.07 RPM
SRP007412_kidney	0.00 RPM	27.03 RPM
SRP007412_liver	0.00 RPM	51.49 RPM
SRP007412_testis	0.10 RPM	20.62 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_2341 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2341 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3469
Pan troglodytes	retro_ptro_2352
Pongo abelii	retro_pabe_2865
Macaca mulatta	retro_mmul_1764
Callithrix jacchus	retro_cjac_2338

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003285	1 retrocopy	retro_cjac_2338,
Homo sapiens	ENSG00000178537	1 retrocopy	retro_hsap_3469,
Gorilla gorilla	ENSGGOG00000028046	1 retrocopy	retro_ggor_2341 ,
Macaca mulatta	ENSMMUG00000015418	1 retrocopy	retro_mmul_1764,
Monodelphis domestica	ENSMODG00000013383	3 retrocopies	retro_mdom_1584, retro_mdom_229, retro_mdom_266,
Nomascus leucogenys	ENSNLEG00000006700	1 retrocopy	retro_nleu_342,
Pongo abelii	ENSPPYG00000013892	1 retrocopy	retro_pabe_2865,
Pan troglodytes	ENSPTRG00000014900	1 retrocopy	retro_ptro_2352,
Drosophila melanogaster	FBgn0031881	1 retrocopy	retro_dmel_15,