RetrogeneDB ID: retro_pabe_3395

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:28672941..28673556(+)
• Located in intron of: ENSPPYG00000019142

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEA1
• Ensembl ID: ENSPPYG00000018589
• Aliases: None
• Description: transcription elongation factor A (SII), 1 [Source:HGNC Symbol;Acc:11612]

Sequence

>retro_pabe_3395
GAGGACAAGGTGGTTCCCATGGCCAAGTAGATGGACAAGATGGTGCAGAAGAATACAGCTGGAGCATTGGATTTGCCAAA
GGAGCTTAAAAATATTCCCACGACCATGGAATTATTACAGCCCCCAGAAGAATCAGAATATCAGTTAATGCTAATGGCAA
GCAGCATAAAGATGAAGAAGTTACATCTTTAACAGTCTGTCATGAAATCTTGGAAAAAGTTACTATCAATCGAGAAAGAC
CCTGAAGAAAAGAAAAAAGAACCTGCAGTTACATTGCAGAATAACCCTGAAGCGAGAGAAGAAAGTAGCTCCGGTGGCAA
TGCAAGCAGCCGAGAGGGTGAGACAAATGTTCTAGATACTCGTGTTTCATCTTTTATTCAGGAACGAAGCACTTCTGACT
CTCTTTGGTTAAAGTGTTGGGAGGTGCTTGCTGCAGCTCTCCAAACAGGAGATGGCTACACTGCTGTTGGAGCTGGTGAG
GAAGAATTAGGATCTCAAATTGAGGAGGCTGTATATCAAGAAGTTAAGGAATATAGATACGAAGTGCAAAAGTAGAGTAT
GAAGTAGGATATCAAATCTTAAAGAGCAAAGAATCCAAATTTAAGGGAAAATGTA

Alignment

ORF - retro_pabe_3395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.98 %
• Parental protein coverage: 69.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDEVVRFAKKMDKMVQKKNAAGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIK
          ED.VV..AK.MDKMVQK.N.AGALDL.KELKNIP.T.ELLQ..............S.......L..S..K
Retrocopy EDKVVPMAK*MDKMVQK-NTAGALDLPKELKNIPTTMELLQPPEESEYQLMLMASSIKMKKLHL*QSVMK

Parental  SWKKLLDGPSTEKDLDEKKKEPAITSQNSPEAREESTSSGNVSNRKDETNARDTYVSSFPRAPSTSDSVR
          SWKKLL...S.EKD..EKKKEPA.T.QN.PEAREES.S.GN.S.R..ETN..DT.VSSF....STSDS..
Retrocopy SWKKLL---SIEKDPEEKKKEPAVTLQNNPEAREESSSGGNASSREGETNVLDTRVSSFIQERSTSDSLW

Parental  LKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEI-RNTDMKYKNRVRSRISNLKD-AKNPNLRKN
          LKC.E.LAAAL.TGD.Y.A.GA.EEELGSQIEEA.YQE..RN.D.K.K.RV.SRISNLK..AKNPNLR.N
Retrocopy LKCWEVLAAALQTGDGYTAVGAGEEELGSQIEEAVYQEV>RNIDTKCKSRV*SRISNLKE<AKNPNLREN

Parental  V
          V
Retrocopy V

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	1.38 RPM	27.31 RPM
SRP007412_cerebellum	3.04 RPM	40.86 RPM
SRP007412_heart	0.15 RPM	20.95 RPM
SRP007412_kidney	0.46 RPM	29.47 RPM
SRP007412_liver	0.49 RPM	32.01 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3395 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3395 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3395 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4243

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395 , retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,