RetrogeneDB ID: retro_ptro_2155

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:59952369..59953103(+)
• Located in intron of: ENSPTRG00000016880

Retrocopy information

• Ensembl ID: ENSPTRG00000041703
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSPTRG00000009956
• Aliases: None
• Description: ring finger protein 138, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17765]

Sequence

>retro_ptro_2155
ATGGCTGAGGACCTCTCCGCGGCCACATCCTACACCAAAGATGATTTCTACTGCCCCGTCTGTCAGGAGGTGCTCAAAAC
GCCCGTGCGGACCGCGGCCTGTCAGCACGTTCTCTGTAGAAAATGTTTCCTGACTGCAATGAGGGAAAGCGGAGCACATT
GTCCCCTGTGTCATGGAAATGTGACTAGAAGAGAGAGAGCATGCCCTGAACGGGCCTTAGACCTTGAAAATATAATGAGG
AAGTTTTCTGGTAGCTGTAGATGCTGTGCAAAACAGATTAAGTTCTATCGCATGAGACATCATTACAAATCTTGTAAGAA
GTATCAGGATGAATATGATGTTTCTTCTATCATTCCAAACTTTCAGATCTCTCAAGATTCAGTAGGGAACAGCAATAGGA
GTGAAACATCCACATCTGATAACACAGAAACTTACCAAAAAATACAAGTTCTTCTGGTCATCCTACTTTTAAGTGTCCCC
TGTGTAAAGAATCAGATTTTACCAAAGAGCGTTTACTGGATCACTCTAACAGTAATCACCTATTTCAGATACTTCCTGTG
ACATGTCCTATTTGTGTGTCTCTTCCTTGGGGAGATCCTAGCCAGATTACCAGAAATTTCGTTAGTCATCTAAATCAGAG
ACATCAGTTTGATTATGGAGAATTTGTGAATCTTCAGGTAGATGAAGAAACCCAATGTCAAACTGCTGTTGAAGAATCTT
CTCAAGTAAACATC

Alignment

ORF - retro_ptro_2155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEDLSAATSYTEDDFYCPVCQEVLKTPVRTTACQHVFCRKCFLTAMRESGAHCPLCRGNVTRRERACPE
          MAEDLSAATSYT.DDFYCPVCQEVLKTPVRT.ACQHV.CRKCFLTAMRESGAHCPLC.GNVTRRERACPE
Retrocopy MAEDLSAATSYTKDDFYCPVCQEVLKTPVRTAACQHVLCRKCFLTAMRESGAHCPLCHGNVTRRERACPE

Parental  RALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVSSIIPNFQISQDSVGNSNRSETSTSD
          RALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEY.VSSIIPNFQISQDSVGNSNRSETSTSD
Retrocopy RALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYDVSSIIPNFQISQDSVGNSNRSETSTSD

Parental  NTETYQ-ENTSSSGHPTFKCPLCQESNFTRQRLLDHCNSNHLFQIVPVTCPICVSLPWGDPSQITRNFVS
          NTETYQ..NTSSSGHPTFKCPLC.ES.FT..RLLDH.NSNHLFQI.PVTCPICVSLPWGDPSQITRNFVS
Retrocopy NTETYQ<KNTSSSGHPTFKCPLCKESDFTKERLLDHSNSNHLFQILPVTCPICVSLPWGDPSQITRNFVS

Parental  HLNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNI
          HLNQRHQFDYGEFVNLQ.DEETQ.QTAVEES.QVNI
Retrocopy HLNQRHQFDYGEFVNLQVDEETQCQTAVEESSQVNI

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	0.14 RPM	3.95 RPM
SRP007412_cerebellum	0.00 RPM	4.02 RPM
SRP007412_heart	0.06 RPM	1.57 RPM
SRP007412_kidney	0.08 RPM	5.65 RPM
SRP007412_liver	0.00 RPM	4.12 RPM
SRP007412_testis	0.21 RPM	84.10 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2155 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2155 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2155 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3319
Pongo abelii	retro_pabe_2734

---

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,