RetrogeneDB ID: retro_ggor_1230

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 16:35048393..35048992(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A1
• Ensembl ID: ENSGGOG00000006198
• Aliases: None
• Description: None

Sequence

>retro_ggor_1230
AGCCACAGCATCCTGGGCCTGGACCGCGGCCTCAACTCCCTGCTCTGCGGCTCCATCCCCGAGGCAGCGTCAGGTTCCGG
ACATTCGAGTTCCTCAGCACCCAGATGCGGGATGCCCAGGGACAGCTAAACAGCAGGCGCGGGCTGCTGTGCGGCCTGGG
CGCCGGCGTGGCCGAGGCCGTGGTGGTCGTCCATCCCATGCAGACCATCAAAGTGAAGTTCATCCACGACCAGACCTCCC
CAAACCCAAGAACAGAGAATTCTTTGGGGTTAGGGAGATTGTGCGGGAACAAGAGCTGAGGGGACTTACCAGGGCCTCAC
GGCCGCCGCGCTGAAGCAGGGCTGGAACCAGGCCATTGCTTCTTCGTCCTGACCTCCCTGCAGCAACTGGTACCGAAGGG
ACAAACCCATAAACCCGCTGATCACTGGGGTCTTCTGAGACATTGCGGGCGCAGCCAGCGTCTTTGGAAATGCCCCTCTG
GACGGGATAGAGATCCGGATGCGCGGCGTGGACGTGCACAAACACCGGAACAGTGGACTGCAGCTGCAGATCCCGAGGAA
GGAGGGGCTCAACGCCTTCACAAGGGCACTGGCCCCCGC

Alignment

ORF - retro_ggor_1230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.11 %
• Parental protein coverage: 66.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SHGVLGLYRGLSSLLYGSIPKAA-VRFGMFEFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVVCPMET
          SH..LGL.RGL.SLL.GSIP.AA.VRF..FEFLS..MRDAQG.L.S.RGLLCGLGAGVAEAVVVV.PM.T
Retrocopy SHSILGLDRGLNSLLCGSIPEAA<VRFRTFEFLSTQMRDAQGQLNSRRGLLCGLGAGVAEAVVVVHPMQT

Parental  IKVKFIHDQTSPN-PKYRGFFHGVREIVREQGLK-GTYQGLTATVLKQGSNQAIR-FFVMTSLR-NWYRG
          IKVKFIHDQTSPN.PK.R.FF.GVREIVREQ.L..GTYQGLTA..LKQG.NQAI..FFV.TSL..NWYR.
Retrocopy IKVKFIHDQTSPN<PKNREFF-GVREIVREQELR<GTYQGLTAAALKQGWNQAIA<FFVLTSLQ>NWYRR

Parental  DNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHKYRNTWDCGLQILRKEGLKAF-YKGTV
          D...KP.NPLITGVF..IAGAASVFGN.PLD.I..RM.G...HK.RN.....LQI.RKEGL.AF..KGT.
Retrocopy D---KPINPLITGVF*DIAGAASVFGNAPLDGIEIRMRGVDVHKHRNS-GLQLQIPRKEGLNAF<HKGTG

Parental  PR
          PR
Retrocopy PR

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	0.05 RPM	22.63 RPM
SRP007412_cerebellum	0.00 RPM	26.44 RPM
SRP007412_heart	0.00 RPM	15.57 RPM
SRP007412_kidney	0.00 RPM	98.58 RPM
SRP007412_liver	0.00 RPM	95.94 RPM
SRP007412_testis	0.00 RPM	52.73 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_1230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1230 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1632
Pongo abelii	retro_pabe_1414

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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,