RetrogeneDB ID: retro_ggor_1685

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2a:59552001..59552996(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IK
• Ensembl ID: ENSGGOG00000013374
• Aliases: None
• Description: None

Sequence

>retro_ggor_1685
ATTCCGGAGCGAGATAGTGAGCCGTTCTCCAACCCTTTGGCCCCTGACGGCCACGATGTGCATGAACCTCACTCCTTTCA
CCAATCAAAACTCACCAATGAAGACTTCAGGAAACTTCTCATGACCCCCAGGGCTGCACCTACCTCTGCACCACCTTCTA
AGTCACGTCACCATGAGATGCCAAGGGAGTACAATGAGGATGAAGACCCAGCTGCACGAAGGAGGAAAAAGAAAAGTTAT
TATGCTAAGCTACGCCAACAAGAAATTGAGAGAGAGAGAGAGCTAGCAGAGAAGTACCGGGGTCATGCCAAGGAACGGAG
AGATGGAGTGAACAAAGATTATGAAGAAACCGAGCTTATCAACACCACAGCTAACTACAGGGCTGTTGGCCCCACTGCTA
AGGCGGACAAATCAGCTGCAGAGAAGAGAAGACAGTTGATCCAGGAGTCCAAATTCTTGGGTGGTGACACGGAACACACC
CATTTGGTGAAAGGCTTGGATTTTGCTCTGCTTCAAAAGGTACGAGCTGAGATTGCCAGCAAAGAGAAAGAGGAAGAGGA
ACTGATGGAAAAGCCCCAGAAAGAAACCAAGAAAGATGAGGATCCTGAAAATAAAACTGAATTTAAAACACGTCTGGGCT
GCAATGTTTACCGAGTGCTTTTTAAGAGCAAGCATATAAGCGGAATGAGTTGTTCCTGACGGGCCGCATGGCCTATGTGG
TAGGCCTGGATGATGAGTAAGCTGACACCGATATCCCCACCACTCTTATCCACAGCAAGGTTGATTGCCCCACCATGGAG
GCCCAGACCATACTGACCACAAATGATATTGTCATTAGCAAGCTTACCCAGTTGCTTTCATACCTGAGGCAGGGAACCCG
TAACAAGAAGCTTAAGAAGAAGGATAAAGGGAAGCTGGAAGACAAGAAACCTCCTGAGGCTGACAGGAGTATTTTCGAAG
ACATTGGGGATTACACACCCTCCACAATCAAGACA

Alignment

ORF - retro_ggor_1685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.99 %
• Parental protein coverage: 64.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPERDSEPFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDP
          .PERDSEPFSNPLAPDGHDV..PHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDP
Retrocopy IPERDSEPFSNPLAPDGHDVHEPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDP

Parental  AARRRKKKSYYAKLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAVGPTAEADKSAA
          AARRRKKKSYYAKLRQQEI.....LAEKYR..AKERRDGVNKDYEETELI.TTANYRAVGPTA.ADKSAA
Retrocopy AARRRKKKSYYAKLRQQEIXXXXXLAEKYRGHAKERRDGVNKDYEETELINTTANYRAVGPTAKADKSAA

Parental  EKRRQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFKT
          EKRRQLIQESKFLGGD.EHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENK.EFKT
Retrocopy EKRRQLIQESKFLGGDTEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKTEFKT

Parental  RLGRNVYRMLFKSK-AYERNELFLPGRMAYVVDLDDEYADTDIPTTLIRSKADCPTMEAQTTLTTNDIVI
          RLG.NVYR.LFKSK.AY.RNELFL.GRMAYVV.LDDE.ADTDIPTTLI.SK.DCPTMEAQT.LTTNDIVI
Retrocopy RLGCNVYRVLFKSK<AYKRNELFLTGRMAYVVGLDDE*ADTDIPTTLIHSKVDCPTMEAQTILTTNDIVI

Parental  SKLTQILSYLRQGTRNKKLKKKDKGKLEEKKPPEADMNIFEDIGDYVPSTTKT
          SKLTQ.LSYLRQGTRNKKLKKKDKGKLE.KKPPEAD..IFEDIGDY.PST.KT
Retrocopy SKLTQLLSYLRQGTRNKKLKKKDKGKLEDKKPPEADRSIFEDIGDYTPSTIKT

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	123.96 RPM
SRP007412_cerebellum	0.12 RPM	131.94 RPM
SRP007412_heart	0.00 RPM	48.78 RPM
SRP007412_kidney	0.08 RPM	102.59 RPM
SRP007412_liver	0.05 RPM	80.48 RPM
SRP007412_testis	0.41 RPM	266.25 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_1685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1685 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2262
Pongo abelii	retro_pabe_1954

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009727	3 retrocopies	retro_dnov_618, retro_dnov_714, retro_dnov_960,
Dipodomys ordii	ENSDORG00000006584	4 retrocopies	retro_dord_128, retro_dord_130, retro_dord_134, retro_dord_139,
Homo sapiens	ENSG00000113141	1 retrocopy	retro_hsap_2262,
Gorilla gorilla	ENSGGOG00000013374	1 retrocopy	retro_ggor_1685 ,
Loxodonta africana	ENSLAFG00000008152	1 retrocopy	retro_lafr_362,
Otolemur garnettii	ENSOGAG00000014281	1 retrocopy	retro_ogar_1402,
Pongo abelii	ENSPPYG00000015861	1 retrocopy	retro_pabe_1954,
Sorex araneus	ENSSARG00000007388	3 retrocopies	retro_sara_416, retro_sara_419, retro_sara_558,