RetrogeneDB ID: retro_pabe_302

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:139551121..139551779(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf74
• Ensembl ID: ENSPPYG00000003347
• Aliases: None
• Description: chromosome 11 open reading frame 74 [Source:HGNC Symbol;Acc:25142]

Sequence

>retro_pabe_302
ATGTCTGCCCATACATCAGGATTGAAAATAATGCGTGAAGATCAATTAATCAAAGAAGTCTTGGATAAATTCCTTAATTG
TCATGAGCAAACATATGATGAAGAATTTCTGAACACTTTTACTCATCTTTCACAAGAGGATCTTGTGTCCAAAAGGGGAG
TGTTTGGAACTGATTCTTCGGAAAACATTTTTACCTACGCAAAGTTACTCATAAAAATGAAGCTAATGACTACCACCTTA
GAAATAAAACCATTTTTCTTCATACTTCATGACAATGTTTGGAAGAACAGGTAGACAATTTCCTAGATTTGGAAGATTTG
GACATGCATGAAGAGATTAAACCCCAAATAAGTGAGGATTTGCTGCTGCTCCCAGGAGAAGTGGAGTAGGATGTAAGCAC
CAGCATTCCTTCCTGTATCCTTCTGTGGCACAGCCTCCCACCTGTGAAGTGAAGCCAAAGCCTACTGTAAAAAGAATGGA
CAAACAGATGGAAGAGATATGTGGAGATGAAGTTCAACCCTTCTCACTTGATGAGGAATTCGATTATGACAATGTGACAC
TAACCTCCAAGTTTAGTCCTGCAGAGATAGAGACCATCAAAGAGCTAGGCAAGCAAAAGAGAAAGGTCACCAGCCCAGAC
TTAGAGGAACCCTGTGAC

Alignment

ORF - retro_pabe_302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSAHMSGLEIMDEDQLIKEVLDKFLNCHEQTCDEEFLNTFTHLSQEDHVSKREVFGTDSSENIFTSAK-V
          MSAH.SGL.IM.EDQLIKEVLDKFLNCHEQT.DEEFLNTFTHLSQED.VSKR.VFGTDSSENIFT.AK.V
Retrocopy MSAHTSGLKIMREDQLIKEVLDKFLNCHEQTYDEEFLNTFTHLSQEDLVSKRGVFGTDSSENIFTYAK<V

Parental  THKNEANDYHLRNKTIFLRTSSQCLEEQVDNFLDLEDLDMDEEIKPQMSEDLLLLPGEVEQDVSTSIPSC
          THKNEANDYHLRNKTIFL.TS.QCLEEQVDNFLDLEDLDM.EEIKPQ.SEDLLLLPGEVE.DVSTSIPSC
Retrocopy THKNEANDYHLRNKTIFLHTS*QCLEEQVDNFLDLEDLDMHEEIKPQISEDLLLLPGEVE*DVSTSIPSC

Parental  I-PFVAQPPTCEVKPKPTVKRMDKQTEEILGDEVQPFSLDEEFDYDNVTLTSKFSPAEIETIKELCKQKR
          I.P.VAQPPTCEVKPKPTVKRMDKQ.EEI.GDEVQPFSLDEEFDYDNVTLTSKFSPAEIETIKEL.KQKR
Retrocopy I<PSVAQPPTCEVKPKPTVKRMDKQMEEICGDEVQPFSLDEEFDYDNVTLTSKFSPAEIETIKELGKQKR

Parental  KDTSPDLEESCD
          K.TSPDLEE.CD
Retrocopy KVTSPDLEEPCD

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	0.17 RPM	7.46 RPM
SRP007412_cerebellum	0.24 RPM	6.20 RPM
SRP007412_heart	0.30 RPM	7.50 RPM
SRP007412_kidney	0.03 RPM	6.76 RPM
SRP007412_liver	0.03 RPM	3.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_302 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_302 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_302 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_418
Pan troglodytes	retro_ptro_320
Gorilla gorilla	retro_ggor_411

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000010963	2 retrocopies	retro_dord_388, retro_dord_615,
Homo sapiens	ENSG00000166352	1 retrocopy	retro_hsap_418,
Gorilla gorilla	ENSGGOG00000004773	1 retrocopy	retro_ggor_411,
Macropus eugenii	ENSMEUG00000003065	1 retrocopy	retro_meug_328,
Microcebus murinus	ENSMICG00000008620	1 retrocopy	retro_mmur_383,
Monodelphis domestica	ENSMODG00000019838	1 retrocopy	retro_mdom_1594,
Pongo abelii	ENSPPYG00000003347	1 retrocopy	retro_pabe_302 ,
Pan troglodytes	ENSPTRG00000003514	2 retrocopies	retro_ptro_2924, retro_ptro_320,
Tupaia belangeri	ENSTBEG00000004277	2 retrocopies	retro_tbel_2155, retro_tbel_2277,