RetrogeneDB ID: retro_pabe_2734

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:56792300..56793035(-)
• Located in intron of: ENSPPYG00000015470

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSPPYG00000009094
• Aliases: None
• Description: ring finger protein 138, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17765]

Sequence

>retro_pabe_2734
GTGGCCGAGGACCTCTCTGTAGCCACGTCCTACACCGAAGATGATTTCTACTGCCCCGTCTGTCAGGAGGTACTCAAAAC
GCCCGTGCGGACCGCGGCCTGTCAGCACGTTTTCTGTAGAAAATGTTTCCTGACTGCAATGAGGGAAAGTGGAGCACATT
GTCCCCTGTGTCGTGGAAATGTGACTAGAAGAGAGAGAGCATGTCCTGAACGGGCCTTAGACCTTGAAAATATAATGAGG
AAGTTTTCTGGTAGCTGCAGATGCTGTGCAAAACAGATTAAATTCTATCGCATGAGACATCATTACAAATCTTGTAAGAA
GTATCAGGATGAATATGATGTTTCTTCTATCATTCCAAACTTTCAGATCTCTCAAGATTCAGTAGGGAACAGCAATAGGA
GTGAAACATCCACATCTGATAACACAGAAACTTACCAAGAGAATACAAGTTCTTCTGGTCATCCTACTTTTAAGTGTCCC
CTGTGTCAAGAATCAGATTTTACCAGAGAGCGTTTACTGGATCACTCTAACAGTAATCACCTATTTCAGATAGTTCCTGT
GACATGTCCTATTTGTGTGTCTCTTCCTTGGGGAGATTCTAGCCAGATTACCGGAAATTTCATTAGCCATCTAAATCAGA
GACATCAGTTTGATTATGGAGAATTTGTGAATCTTCAGCTAGATGAAGAAACCCAATATCAAACTGCTGTTGAAGAATCT
TTTCAAGTAAACATC

Alignment

ORF - retro_pabe_2734 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEDLSAATSYTEDDFYCPVCQEVLKTPVRTTACQHVFCRKCFLTAMRESGAHCPLCRGNVTRRERACPE
          .AEDLS.ATSYTEDDFYCPVCQEVLKTPVRT.ACQHVFCRKCFLTAMRESGAHCPLCRGNVTRRERACPE
Retrocopy VAEDLSVATSYTEDDFYCPVCQEVLKTPVRTAACQHVFCRKCFLTAMRESGAHCPLCRGNVTRRERACPE

Parental  RALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVSSIIPNFQISQDSVGNSNRSETSTSD
          RALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEY.VSSIIPNFQISQDSVGNSNRSETSTSD
Retrocopy RALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYDVSSIIPNFQISQDSVGNSNRSETSTSD

Parental  NTETYQENTSSSGHPTFKCPLCQESNFTRQRLLDHCNSNHLFQIVPVTCPICVSLPWGDPSQITRNFVSH
          NTETYQENTSSSGHPTFKCPLCQES.FTR.RLLDH.NSNHLFQIVPVTCPICVSLPWGD.SQIT.NF.SH
Retrocopy NTETYQENTSSSGHPTFKCPLCQESDFTRERLLDHSNSNHLFQIVPVTCPICVSLPWGDSSQITGNFISH

Parental  LNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNI
          LNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNI
Retrocopy LNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNI

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	0.06 RPM	1.49 RPM
SRP007412_cerebellum	0.12 RPM	3.53 RPM
SRP007412_heart	0.03 RPM	1.63 RPM
SRP007412_kidney	0.36 RPM	2.82 RPM
SRP007412_liver	0.46 RPM	4.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2734 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2734 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2734 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3319
Pan troglodytes	retro_ptro_2155

---

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,