RetrogeneDB ID: retro_pabe_1928

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:14276348..14277194(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf106
• Ensembl ID: ENSPPYG00000016519
• Aliases: None
• Description: chromosome 6 open reading frame 106 [Source:HGNC Symbol;Acc:21215]

Sequence

>retro_pabe_1928
ATGGAGGGCATGGACATGGACCGGGACCTGGAGCTGATGCAGAATTTCAGCTGCCTGAGCACCACCAACAAGGACGTGCT
CATCTCCGAGTTCCAGAGGCTGTTCAGCTTCCAGCTCAACCCTGGCAGTTGCGCCTTCTTCCTGGACAGGACCAACTGGA
ACCTACAAGCAGCAATTGGTGCCTCTTATGCCTTTGAGAGCTCAAACATCAGTGTGCCCTCTATGTCCTTTGTTGAAGAT
GTCACCATAGAGGAAGGGTAGTCAATACCTCCTGATACTCAGTTTGTAAAAACATGGTAGATCCAGAATTCTGGGACGGA
GGCCTGGCCTCCAGGGGTTTGTCTTAAATATGTCGGGGGAGACCAAGTTGGACATGTGAACATGCTGATGGTGAGACTGC
TAGAGCCGCAAGAGATTACAGATGTTATTGTCCAGATGTGCAGCCCCGGCAGAGCAGGAATGTATCAGGGATGGTGACGG
ATGTGCACTGCTACAGGACTCTACTATGGAGATGTCATCTGGGTGATTCTCAGTGTGGAGGTGGGTGGACTTTTAGAAAT
AACACAGCAGCTGTCATCTTTTGAAACGGAGTTCAACACACAGCCGCATAGCAAGGTAGAAGGAAACTTCAACCCTTTTG
CCTCTCCCCAAAAGAACCAACAATCAGATGAAAACAACTTATAAGTCCCTGGGGGTTCCAAGTTCTACTCGATCAGCAAA
AACACATGGGCTCCTGCTCCTGACCAAACTGAGCAAGACCAGGGCAGACTGTCACAGAACTCTGTAAATCTGTCTCCCAG
CCGTCATGCAAACAACTTATCAGTAGTGACTTACAGTAAGGGGCTC

Alignment

ORF - retro_pabe_1928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.01 %
• Parental protein coverage: 93.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGMDVDLDPELMQKFSCLGTTDKDVLISEFQRLLGFQLNPAGCAFFLDMTNWNLQAAIGAYYDFESPNI
          MEGMD.D.D.ELMQ.FSCL.TT.KDVLISEFQRL..FQLNP..CAFFLD.TNWNLQAAIGA.Y.FES.NI
Retrocopy MEGMDMDRDLELMQNFSCLSTTNKDVLISEFQRLFSFQLNPGSCAFFLDRTNWNLQAAIGASYAFESSNI

Parental  SVPSMSFVEDVTIGEGESIPPDTQFVKTWRIQNSGAEAWPPGVCLKYVGGDQFGHVNMVMVRSLEPQEIA
          SVPSMSFVEDVTI.EG.SIPPDTQFVKTW.IQNSG.EAWPPGVCLKYVGGDQ.GHVNM.MVR.LEPQEI.
Retrocopy SVPSMSFVEDVTIEEG*SIPPDTQFVKTW*IQNSGTEAWPPGVCLKYVGGDQVGHVNMLMVRLLEPQEIT

Parental  DVSVQMCSPSRAGMYQGQWRMCTATGLYYGDVIWVILSVEVGGLLGVTQQLSSFETEFNTQPHRKVEGNF
          DV.VQMCSP.RAGMYQG..RMCTATGLYYGDVIWVILSVEVGGLL..TQQLSSFETEFNTQPH.KVEGNF
Retrocopy DVIVQMCSPGRAGMYQGW*RMCTATGLYYGDVIWVILSVEVGGLLEITQQLSSFETEFNTQPHSKVEGNF

Parental  NPFASPQKNRQSDENNLKDRGGSEFDSISKNTWAPAPDTWAPAPDQTEQDQNRL--SQNSVNLSPSSHAN
          NPFASPQKN.QSDENNL...GGS.F.SISKNTWAPAPD..........Q....L..S....NLS......
Retrocopy NPFASPQKNQQSDENNL*VPGGSKFYSISKNTWAPAPDQTEQDQGRLSQNSVNLSPSRHANNLSVVTYSK

Parental  NL
          .L
Retrocopy GL

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	0.00 RPM	220.17 RPM
SRP007412_cerebellum	0.00 RPM	220.83 RPM
SRP007412_heart	0.00 RPM	60.33 RPM
SRP007412_kidney	0.00 RPM	111.84 RPM
SRP007412_liver	0.03 RPM	75.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1928 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1928 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1928 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034493	1 retrocopy	retro_btau_1343,
Callithrix jacchus	ENSCJAG00000015304	1 retrocopy	retro_cjac_2788,
Homo sapiens	ENSG00000196821	1 retrocopy	retro_hsap_2137,
Gorilla gorilla	ENSGGOG00000000388	1 retrocopy	retro_ggor_1653,
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Macaca mulatta	ENSMMUG00000022824	1 retrocopy	retro_mmul_2155,
Nomascus leucogenys	ENSNLEG00000008387	2 retrocopies	retro_nleu_1933, retro_nleu_2739,
Otolemur garnettii	ENSOGAG00000011264	1 retrocopy	retro_ogar_3245,
Ochotona princeps	ENSOPRG00000009350	1 retrocopy	retro_opri_559,
Pongo abelii	ENSPPYG00000016519	2 retrocopies	retro_pabe_1265, retro_pabe_1928 ,
Pan troglodytes	ENSPTRG00000018068	1 retrocopy	retro_ptro_1564,