RetrogeneDB ID: retro_ggor_1302

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:41674133..41674869(+)
• Located in intron of: ENSGGOG00000001872

Retrocopy information

• Ensembl ID: ENSGGOG00000000661
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSGGOG00000027857
• Aliases: None
• Description: None

Sequence

>retro_ggor_1302
ATGGCTGAGGACCTCTCCGCGGCCACATCCTACACCAAAGATGATTTCTACTGCCCCGTCTGTCAGGAGGTGCTCAAAAC
GCCCGTGCGGACCACGGCCTGTCAGCACGTTTTCTGTAGAAAATGTTTCCTGACTGCAATGAGGGAAAGCGGAGCACATT
GTCCCCTGTGTCGTGGAAATGTGACTAGAAGAGAGAGAGCATGTCCTGAACGGGCCTTAGACCTTGAAAATATAATGAGG
AAGTTTTCTGGTAGCTGCAGATGCTGTGCAAAGCAGATTAAATTCTATCGCATGAGACTTCATTACAAATCTTGTAAGAA
GTATCAGGATGAATATGATGTTTCTTCTATCATTCCAAACTTTCAGATCTCTCAAGATTCAGTAGGGAACAGCAATAGGA
GTGAAACATCCACATCTGATAACACAGAAACTTACCAAGAGAATACAAGTTCTTCTGGTCATCCTACTTTTAAGTGTCCC
CTGTGTCAAGAATCAAATTTTACCAGAGAGCGTTTACTGGATCACTCTTAACAGTAATCACCTATTTCAGATAGTTCCTG
TGACATGTCCTATTTGTGTGTCTCTTCCTTGGGGAGATCCTAGCCAGATTACCAGAAATTTCGTTAGTCATCTAAATCAG
AGACATCAGTTTGATTATGGAGAATTTGTGAATCTTCAGCTAGATGAAGAAACCCAATGTCAAACTGCTGTTGAAGAATC
TTTTCAAGTAAACATC

Alignment

ORF - retro_ggor_1302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEDLSAATSYTEDDFYCPVCQEVLKTPVRTTACQHVFCRKCFLTAMRESGAHCPLCRGNVTRRERACPE
          MAEDLSAATSYT.DDFYCPVCQEVLKTPVRTTACQHVFCRKCFLTAMRESGAHCPLCRGNVTRRERACPE
Retrocopy MAEDLSAATSYTKDDFYCPVCQEVLKTPVRTTACQHVFCRKCFLTAMRESGAHCPLCRGNVTRRERACPE

Parental  RALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVSSIIPNFQISQDSVGNSNRSETSTSD
          RALDLENIMRKFSGSCRCCAKQIKFYRMR.HYKSCKKYQDEY.VSSIIPNFQISQDSVGNSNRSETSTSD
Retrocopy RALDLENIMRKFSGSCRCCAKQIKFYRMRLHYKSCKKYQDEYDVSSIIPNFQISQDSVGNSNRSETSTSD

Parental  NTETYQENTSSSGHPTFKCPLCQESNFTRQRLLDH-CNSNHLFQIVPVTCPICVSLPWGDPSQITRNFVS
          NTETYQENTSSSGHPTFKCPLCQESNFTR.RLLDH..NSNHLFQIVPVTCPICVSLPWGDPSQITRNFVS
Retrocopy NTETYQENTSSSGHPTFKCPLCQESNFTRERLLDH>LNSNHLFQIVPVTCPICVSLPWGDPSQITRNFVS

Parental  HLNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNI
          HLNQRHQFDYGEFVNLQLDEETQ.QTAVEESFQVNI
Retrocopy HLNQRHQFDYGEFVNLQLDEETQCQTAVEESFQVNI

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	1.25 RPM
SRP007412_cerebellum	0.16 RPM	2.17 RPM
SRP007412_heart	0.03 RPM	0.50 RPM
SRP007412_kidney	0.16 RPM	2.25 RPM
SRP007412_liver	0.18 RPM	3.35 RPM
SRP007412_testis	0.41 RPM	44.13 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_1302 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1302 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020160	1 retrocopy	retro_btau_322,
Choloepus hoffmanni	ENSCHOG00000012689	6 retrocopies	retro_chof_1043, retro_chof_1242, retro_chof_1931, retro_chof_418, retro_chof_714, retro_chof_793,
Callithrix jacchus	ENSCJAG00000020875	1 retrocopy	retro_cjac_2325,
Felis catus	ENSFCAG00000014180	2 retrocopies	retro_fcat_1383, retro_fcat_379,
Homo sapiens	ENSG00000134758	1 retrocopy	retro_hsap_3319,
Gorilla gorilla	ENSGGOG00000027857	1 retrocopy	retro_ggor_1302 ,
Loxodonta africana	ENSLAFG00000003811	1 retrocopy	retro_lafr_408,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mustela putorius furo	ENSMPUG00000006982	1 retrocopy	retro_mputfur_276,
Nomascus leucogenys	ENSNLEG00000006401	1 retrocopy	retro_nleu_1665,
Pongo abelii	ENSPPYG00000009094	1 retrocopy	retro_pabe_2734,
Pan troglodytes	ENSPTRG00000009956	1 retrocopy	retro_ptro_2155,
Pteropus vampyrus	ENSPVAG00000003778	2 retrocopies	retro_pvam_1316, retro_pvam_1379,
Rattus norvegicus	ENSRNOG00000015645	3 retrocopies	retro_rnor_2316, retro_rnor_808, retro_rnor_965,
Ictidomys tridecemlineatus	ENSSTOG00000002293	2 retrocopies	retro_itri_1443, retro_itri_576,