RetrogeneDB ID: retro_ptro_1364

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:32881640..32882239(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A1
• Ensembl ID: ENSPTRG00000014057
• Aliases: None
• Description: None

Sequence

>retro_ptro_1364
TTCCTCAGCAACCACATGCGGGATGCCCAGGGACTGGTGAACAGCAAGGCGGGCAGCGGTGCGGCCAGTGAGCTAGCGTG
GCCGAGGCCGTGGTGGTCCTATGGCCCATGGAGACCATCAAGGTGAAGTTAATCCATGGTCAGACCTCTCCAAATCCAAG
TACAGGGGATTCTTCCACAGGGTTAGGAGATTGTGCGGGAACACCGGGACTTACCGGGGTCCCACAGGCCCCGCGCTGAA
GGAGGGCTGGAACCAGGCAACTTGTTTCTTTGTCCTGACATCCCTGCGCAGCTGGTACCGAGCGGACAACCCCAACAAAC
TCATGAACTCGCTGGTCGCTGGGGTCTTCGGAGCCATTGTGGGAGCGGCCAGTGTCTTCGGAAATGCTCCTCTGCACGAG
ATCGAGCCCCAGATGCGGGACCTGGAGGCGCACAAATGCAGAACACATGGGACTGTGGCTGCAAATCCTGAGGGAAGGGC
ACAAGACCTTCTACAAGGGCACTATTGCCCGCCTGGGCCGGGTCTGCCTGCATGTGGCCATAGTGTTTATCATCTATGAT
GAGGTGAGGAAGCTGCTCAACAAAGTGTGGAAGACAGAG

Alignment

ORF - retro_ptro_1364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.33 %
• Parental protein coverage: 65.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FLSNHMRDAQGRLDSTRGL-LCGLGAGVAEAVVVVCPMETIKVKFIHDQTSPNP-KYRGFFHGVREIVRE
          FLSNHMRDAQG...S..G...CG..A.VAEAVVV..PMETIKVK.IH.QTSPNP.KYRGFFH.VR.....
Retrocopy FLSNHMRDAQGLVNSKAGS<RCGQ*ASVAEAVVVLWPMETIKVKLIHGQTSPNP<KYRGFFHRVRRLC--

Parental  QGLKGTYQGLTATVLKQGSNQAIRFFVMTSLRNWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVI
          .G..GTY.G.T...LK.G.NQA..FFV.TSLR.WYR.DNPNK.MN.L..GVFGAI.GAASVFGN.PL..I
Retrocopy -GNTGTYRGPTGPALKEGWNQATCFFVLTSLRSWYRADNPNKLMNSLVAGVFGAIVGAASVFGNAPLHEI

Parental  KTRMQGLEAHKYR-NTWDCG-LQILRKEGLKAFYKGTVPRLGRVCLDVAIVFVIYDEVVKLLNKVWKTD
          ...M..LEAHK.R.NTWDCG.LQILR.EG.K.FYKGT..RLGRVCL.VAIVF.IYDEV.KLLNKVWKT.
Retrocopy EPQMRDLEAHKCR<NTWDCG<LQILR-EGHKTFYKGTIARLGRVCLHVAIVFIIYDEVRKLLNKVWKTE

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	25.17 RPM
SRP007412_cerebellum	0.00 RPM	15.24 RPM
SRP007412_heart	0.00 RPM	6.88 RPM
SRP007412_kidney	0.00 RPM	221.01 RPM
SRP007412_liver	0.00 RPM	129.95 RPM
SRP007412_testis	0.00 RPM	15.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1364 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1364 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2047

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100075	2 retrocopies	retro_hsap_1632, retro_hsap_804,
Gorilla gorilla	ENSGGOG00000006198	2 retrocopies	retro_ggor_1230, retro_ggor_661,
Macaca mulatta	ENSMMUG00000005431	4 retrocopies	retro_mmul_1077, retro_mmul_1556, retro_mmul_1683, retro_mmul_485,
Nomascus leucogenys	ENSNLEG00000005215	2 retrocopies	retro_nleu_2866, retro_nleu_408,
Ochotona princeps	ENSOPRG00000011649	1 retrocopy	retro_opri_1053,
Pongo abelii	ENSPPYG00000029785	9 retrocopies	retro_pabe_1346, retro_pabe_1414, retro_pabe_1529, retro_pabe_1671, retro_pabe_3125, retro_pabe_3217, retro_pabe_334, retro_pabe_3564, retro_pabe_719,
Pan troglodytes	ENSPTRG00000014057	3 retrocopies	retro_ptro_1139, retro_ptro_1364 , retro_ptro_560,
Tursiops truncatus	ENSTTRG00000006845	1 retrocopy	retro_ttru_228,