RetrogeneDB ID: retro_pabe_357

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:6860794..6861262(-)
• Located in intron of: ENSPPYG00000000064

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSPPYG00000016529
• Aliases: None
• Description: ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]

Sequence

>retro_pabe_357
AGGCTTAAGTCCACTCCCCACTCCAAGTTCTCTGTGTGTGTCCTGGGGAAACAGCAGCACTGTAACGAGGCCAAGGCTGT
GGATATCCCACACGTGGACATCGAGGTGCTGAAAACACTCAACCAGAATAAGAAACTAGTCAAGAAGCTGGCCAAGAAGT
AGGATGCCCTTTTGGCATCTGAGTCTCTAATCAAGCAGATCCCATAAGTCCTCGGCCCAGGCCTACATAAGGCTGGCACG
TTCCCTTCCCTGCTGATACACAATGAAAATGAAGTGGATGAGGTGAAGTCCACAATGAAGTTCCAGATGACAAAGGTGCT
GTGTCTGGCTGTGGCTGCTGGCCATGTAAATGTTACAGACAACAGGCTTGTGTATTACATTCAACTGACTGTCAACTTCC
TGGTGTCATTACTCAAAAATTGGCACAATGTCTAGGCTTTATATATCAAGTGCACCATGGGCAAGCCC

Alignment

ORF - retro_pabe_357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.75 %
• Parental protein coverage: 83.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLKSTPRPKFSVCVLGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRI
          .LKSTP..KFSVCVLG.QQHC.EAKAVDIPH.DIE.LK.LN.NKKLVKKLAKK.DA.LASESLIKQIP..
Retrocopy RLKSTPHSKFSVCVLGKQQHCNEAKAVDIPHVDIEVLKTLNQNKKLVKKLAKK*DALLASESLIKQIP*V

Parental  LGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSL
          LGPGL.KAG.FPSLL.HNEN....VDEVKST.KFQM.KVLCLAVA.GHV..TD..LVY.I.L.VNFLVSL
Retrocopy LGPGLHKAGTFPSLLIHNEN---EVDEVKSTMKFQMTKVLCLAVAAGHVNVTDNRLVYYIQLTVNFLVSL

Parental  LKKNWQNVRALYIKSTMGKP
          L.KNW.NV.ALYIK.TMGKP
Retrocopy L-KNWHNV*ALYIKCTMGKP

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	74.53 RPM
SRP007412_cerebellum	0.00 RPM	76.12 RPM
SRP007412_heart	0.00 RPM	94.83 RPM
SRP007412_kidney	0.00 RPM	196.86 RPM
SRP007412_liver	0.00 RPM	146.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_357 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_357 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_357 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_337
Pan troglodytes	retro_ptro_269
Gorilla gorilla	retro_ggor_358
Macaca mulatta	retro_mmul_583

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000014090	2 retrocopies	retro_ecab_512, retro_ecab_517,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Mus musculus	ENSMUSG00000037805	8 retrocopies	retro_mmus_1110, retro_mmus_1304, retro_mmus_1422, retro_mmus_149, retro_mmus_1737, retro_mmus_2038, retro_mmus_2652, retro_mmus_452,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Pongo abelii	ENSPPYG00000016529	10 retrocopies	retro_pabe_1208, retro_pabe_1597, retro_pabe_2614, retro_pabe_2759, retro_pabe_3302, retro_pabe_3315, retro_pabe_3377, retro_pabe_357 , retro_pabe_451, retro_pabe_475,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Sus scrofa	ENSSSCG00000001543	7 retrocopies	retro_sscr_1169, retro_sscr_1174, retro_sscr_120, retro_sscr_246, retro_sscr_379, retro_sscr_461, retro_sscr_465,