RetrogeneDB ID: retro_ptro_2352

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:52962553..52963453(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A20
• Ensembl ID: ENSPTRG00000014900
• Aliases: None
• Description: None

Sequence

>retro_ptro_2352
ATAGCCGACCAGCCAAAGCCCATCAGCCTGCTCAAGAACCTGCTGGCCAGTGGCTTTGGTGGCATGTGCCTGGTGTTCAT
GGGGCACCCTCTGGACACTGTCAAGATCCGACTGCAGACACAGCCACCGAGTTTGCCTAGACAGCCTCCCATGTACTCTG
GGACTTTTGACTGTCTCCCAAAGACTCTTAGAAGGGACATCACAGGGCTATATAAGGGAATGGCTGCCCCTATCATCGGT
GTCACCCCCATCTTTGCTGTGTGCTTCTTTGGGTTTGGTTTGAGGAAGAAACTATGACAGAAACACCCAGAAGATGTGCT
CAGCTATCCCCAGCTGTTTGCAGCTGGGATGTTATCTGGTACATTCACCACAGGCATCGCGACCCCTGGAGAACCCATCA
AGTCCTTGTTACACTTTCAGCCTTCTTCAGGGGAAACCAAGTACACTGGAACCTTGGACTGTGCAAAGAAGTTGTACCAG
GAGTTTCAGATCCGAGGCATCTACAAAGGGACCGTGCTTACCCTTATGTGAGATGTTCCAGCTAGCGGAACGTATTTCAT
GACAAATGAATGGCTAAAAAATATCTTCACTCCGGAAGGAAAGAGGGTCTGTGAGCTCAGTGTGCCTTGAATCCTGGTGG
CTGGGTGCATTGCAGGGATCTTCAACTGGGCAATGGCAGTCCCGCAAGATGTGCTCAAATCTCCCTTCCAGACTGCACCA
CTTGGGAAATATCCTAACAGTTTTGGAGATGTGCTGAGGGAGCTGATCTGGGATGAAGGAATCACATCCTTGTCTAAAGG
GTCTGATGCAGTGATGACCCGAGCCTTCCCAGCCAATGCAGCCTGTTTCCTTGGCCTTGAAGTTGCCATGAAGTTTCTTA
ATTGGGCCACCCCCAACTTG

Alignment

ORF - retro_ptro_2352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADQPKPISPLKNLLAGGFGGVCLVFVGHPLDTVKVRLQTQPPSLPGQPPMYSGTFDCFRKTLFREGITG
          .ADQPKPIS.LKNLLA.GFGG.CLVF.GHPLDTVK.RLQTQPPSLP.QPPMYSGTFDC..KTL.R..ITG
Retrocopy IADQPKPISLLKNLLASGFGGMCLVFMGHPLDTVKIRLQTQPPSLPRQPPMYSGTFDCLPKTLRRD-ITG

Parental  LYRGMAAPIIGVTPMFAVCFFGFGLGKKLQQKHPEDVLSYPQLFAAGMLSGVFTTGIMTPGERIKCLLQI
          LY.GMAAPIIGVTP.FAVCFFGFGL.KKL.QKHPEDVLSYPQLFAAGMLSG.FTTGI.TPGE.IK.LL..
Retrocopy LYKGMAAPIIGVTPIFAVCFFGFGLRKKL*QKHPEDVLSYPQLFAAGMLSGTFTTGIATPGEPIKSLLHF

Parental  QASSGESKYTGTLDCAKKLYQEFGIRGIYKGTVLTLMRDVPASGMYFMTYEWLKNIFTPEGKRVSELSAP
          Q.SSGE.KYTGTLDCAKKLYQEF.IRGIYKGTVLTLM.DVPASG.YFMT.EWLKNIFTPEGKRV.ELS.P
Retrocopy QPSSGETKYTGTLDCAKKLYQEFQIRGIYKGTVLTLM*DVPASGTYFMTNEWLKNIFTPEGKRVCELSVP

Parental  RILVAGGIAGIFNWAVAIPPDVLKSRFQTAPPGKYPNGFRDVLRELIRDEGVTSLYKGFNAVMIRAFPAN
          .ILVAG.IAGIFNWA.A.P.DVLKS.FQTAP.GKYPN.F.DVLRELI.DEG.TSL.KG..AVM.RAFPAN
Retrocopy *ILVAGCIAGIFNWAMAVPQDVLKSPFQTAPLGKYPNSFGDVLRELIWDEGITSLSKGSDAVMTRAFPAN

Parental  AACFLGFEVAMKFLNWATPNL
          AACFLG.EVAMKFLNWATPNL
Retrocopy AACFLGLEVAMKFLNWATPNL

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	4.18 RPM
SRP007412_cerebellum	0.00 RPM	1.40 RPM
SRP007412_heart	0.00 RPM	15.13 RPM
SRP007412_kidney	0.00 RPM	11.74 RPM
SRP007412_liver	0.00 RPM	33.45 RPM
SRP007412_testis	0.00 RPM	12.33 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2352 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2352 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3469
Gorilla gorilla	retro_ggor_2341
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,