RetrogeneDB ID: retro_ggor_1962

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:106242571..106243411(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000179295
• Ensembl ID: ENSGGOG00000010689
• Aliases: None
• Description: None

Sequence

>retro_ggor_1962
ATGACATCATGGAAATGGTTTCACCCAAATATCACTGGTGTGGAGGCAGAAAACCTACTGTTGACAAGAGGAGTTGATCG
CAGTTTTTGGGCAAGGCCTAGTAAAAGTAACCCTGGAGACTTCACACTTTCTGTTAGAAGAAATGGAGCTGTCACCCACA
CCAAGATTCAGAACACTGGTGATTGCTATGACCTGTATGGAGGGGAGAAGTTTGCCACTTTGGCTGAGTTGGTCCAGTAT
TACATGGAACATCGTGGGCAATTAAAAGAGAAGAATGGAGATGTTATTGAGCTTAAAAATCCTCTGAACTGTGCAGATCC
TACCTCTGAAAGGTGGTTTCATGGACACCTCTCTGGGAAAGAAGCAGAGAAATTATTAACTGAAAAAGGAAAGCATAGTA
GCTTTCTTGTATGAGAGAGCCAGAGCCACCCTGGAGATTTTGTTCTCTCCGTGTGCACCGGTGATGACAAAGGAGAGAGC
AATGACGGCAAGTCTAAAGTGACTCATGTCATGATTCACTGTCAGGAACTGAAATACGATGTTGGTGGAGGAGAACGGTT
TGATGCTTTGACAGATCTTGTGGAACATTAGAAGAAGAATCCTATGGTGGAAACATTGGGTACAGTACTACAACTCAAGC
AGCCCCTTAACACGACTTGTACAAATGCTGCTGAAATAGAAAGCAGAGTTCGAGAACTAAGCAAATTAGCTGAGACCACA
GATAAAGTCAGACAAGGCTTTTGGGAAGAATTTGAGACACTGCAACAACAGGAGTGCAAACTTCTCTACAGCCAAAAAGA
GGGTCGAAGGCAAGAGAACAAAACCAAAAATAGATATAAA

Alignment

ORF - retro_ggor_1962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 54.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEK
          MTS..WFHPNITGVEAENLLLTRGVD.SF.ARPSKSNPGDFTLSVRRNGAVTH.KIQNTGD.YDLYGGEK
Retrocopy MTSWKWFHPNITGVEAENLLLTRGVDRSFWARPSKSNPGDFTLSVRRNGAVTHTKIQNTGDCYDLYGGEK

Parental  FATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRES
          FATLAELVQYYMEH.GQLKEKNGDVIELK.PLNCADPTSERWFHGHLSGKEAEKLLTEKGKH.SFLV.ES
Retrocopy FATLAELVQYYMEHRGQLKEKNGDVIELKNPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHSSFLV*ES

Parental  QSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVL
          QSHPGDFVLSV.TGDDKGESNDGKSKVTHVMI.CQELKYDVGGGERFD.LTDLVEH.KKNPMVETLGTVL
Retrocopy QSHPGDFVLSVCTGDDKGESNDGKSKVTHVMIHCQELKYDVGGGERFDALTDLVEH*KKNPMVETLGTVL

Parental  QLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYK
          QLKQPLNTT..NAAEIESRVRELSKLAETTDKV.QGFWEEFETLQQQECKLLYS.KEG.RQENK.KNRYK
Retrocopy QLKQPLNTTCTNAAEIESRVRELSKLAETTDKVRQGFWEEFETLQQQECKLLYSQKEGRRQENKTKNRYK

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	0.10 RPM	66.56 RPM
SRP007412_cerebellum	0.04 RPM	34.51 RPM
SRP007412_heart	0.25 RPM	13.76 RPM
SRP007412_kidney	0.08 RPM	18.28 RPM
SRP007412_liver	0.00 RPM	7.68 RPM
SRP007412_testis	0.10 RPM	33.98 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_1962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1962 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012464	1 retrocopy	retro_cjac_1051,
Homo sapiens	ENSG00000179295	5 retrocopies	retro_hsap_2823, retro_hsap_3061, retro_hsap_3302, retro_hsap_3670, retro_hsap_4062,
Gorilla gorilla	ENSGGOG00000010259	2 retrocopies	retro_ggor_453, retro_ggor_925,
Gorilla gorilla	ENSGGOG00000010689	1 retrocopy	retro_ggor_1962 ,
Macaca mulatta	ENSMMUG00000013253	4 retrocopies	retro_mmul_1501, retro_mmul_1792, retro_mmul_1877, retro_mmul_2345,
Monodelphis domestica	ENSMODG00000003120	1 retrocopy	retro_mdom_516,
Nomascus leucogenys	ENSNLEG00000000078	5 retrocopies	retro_nleu_1200, retro_nleu_1360, retro_nleu_1654, retro_nleu_522, retro_nleu_561,
Pongo abelii	ENSPPYG00000004976	4 retrocopies	retro_pabe_2205, retro_pabe_2535, retro_pabe_2825, retro_pabe_3336,