RetrogeneDB ID: retro_pabe_2344

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:128961903..128962818(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSPPYG00000019477
• Aliases: None
• Description: RAD23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:9813]

Sequence

>retro_pabe_2344
ATGGTGAACAAACCCAAAGCAGTGTCCACACCAGCACCAGCTACAACTCAGCAGTCAGCTCCTGCCAGCACTACAGCAGT
TACTTCCTCCACAGCAACAACTGTGGCTCAGGTTCCAACCTCTGTCCCTGCTTTGGCTCCCACTTTCACACCTGCATTCA
TCACTCCAGTATTAATGACAGTGTCTTCTGAACCTGCACCTGCTAGTGCAACTAAACAAGAGAAACCTGCAGAAAAGCCA
GCAGAGACACCAGTGGCTACTAGCCCGACATCAACTCATAGTACCTCGGGAGATTCTTCTTGGTCAAACCTTTTTGAAGA
TGCAATGAATGCACTTGTGATGGGTCAGTCTTACGAGAATATGGTAACTGAGATCATGTCAATGGGCTATGAACGAGAAC
AAGTAATTGCAGCCCCAAGAGCCAGTTTCAACAACCCTGACAGGGCAGTGGAGTACTTTTTAATGGGAATCCCTGGAGAT
AAAGTCAGGTTGTGGTTGACCCCCACCAAGCAGCTAGTACTGGGGCTCCTCAGTCTTCAACAGTGACTGCAGCTGCAGCA
ACTATGACAGCAACAACTACAGCAAGTTCTGGAACATCCCCTTGAATTTTTATGGAATCAGCCTCAGTTTCAACAGATGA
GACAAATTCTTCAACAGAATCCTTCCCTTCTTCCAGCGTTACTACAGTAGATAGATCGAGAGAATCCTCAATTACTTCAG
CAAATTAGCCAACACCAGGAGCATTTTATTCAGATGTTAAATGAAACAGTTCGAGAAGCTGGTGGTCAAAGAGGAAGAGG
TGGAGGTAGCAGTGGAGGAATTGCAGAAGCTGGAAATGGTCCTATGAACTACATTCAAGTAACGCCTCAGGAAAAAGAAG
CTATGGAAAGGTTAAAGGCATTAGGATTCCCTGAA

Alignment

ORF - retro_pabe_2344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.24 %
• Parental protein coverage: 91.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVTKPKAVSTPAPATTQQSAPASTTAVTSSTTTTVAQAPTPVPALAPTSTPASITPASATASSEPASASA
          MV.KPKAVSTPAPATTQQSAPASTTAVTSST.TTVAQ.PT.VPALAPT.TPA.ITP...T.SSEPA.ASA
Retrocopy MVNKPKAVSTPAPATTQQSAPASTTAVTSSTATTVAQVPTSVPALAPTFTPAFITPVLMTVSSEPAPASA

Parental  AKQEKPAEKPAETPVATSPTATDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAALR
          .KQEKPAEKPAETPVATSPT.T.STSGDSS.SNLFEDA..ALV.GQSYENMVTEIMSMGYEREQVIAA.R
Retrocopy TKQEKPAEKPAETPVATSPTSTHSTSGDSSWSNLFEDAMNALVMGQSYENMVTEIMSMGYEREQVIAAPR

Parental  ASFNNPDRAVEYLLM-GIPGDRESQAVVDPPQAASTGAPQSSAVAAAAATTTATTTTTSSGGHP-LEF-L
          ASFNNPDRAVEY.LM.G.P..R.SQ.VVDP.QAASTGAPQSS.V.AAAAT.TA.TTT.SSG..P.L.F.L
Retrocopy ASFNNPDRAVEYFLM<GNPW-R*SQVVVDPHQAASTGAPQSSTVTAAAATMTA-TTTASSGTSP<LNF<L

Parental  RNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGGSGGI
          .NQPQFQQMRQI.QQNPSLLPALLQ.I.RENPQLLQQISQHQEHFIQMLNE.V.EAGGQ.G.GGG.SGGI
Retrocopy WNQPQFQQMRQILQQNPSLLPALLQ*IDRENPQLLQQISQHQEHFIQMLNETVREAGGQRGRGGGSSGGI

Parental  AEAGSGHMNYIQVTPQEKEAIERLKALGFPE
          AEAG.G.MNYIQVTPQEKEA.ERLKALGFPE
Retrocopy AEAGNGPMNYIQVTPQEKEAMERLKALGFPE

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	96.10 RPM
SRP007412_cerebellum	0.12 RPM	107.50 RPM
SRP007412_heart	0.09 RPM	63.79 RPM
SRP007412_kidney	0.10 RPM	66.86 RPM
SRP007412_liver	0.00 RPM	84.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2344 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2344 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2344 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2611

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344 , retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,