RetrogeneDB ID: retro_pabe_1344

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:14668277..14668861(+)
• Located in intron of: ENSPPYG00000007122

Retrocopy information

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

Parental gene information

• Parental gene symbol: TVP23A
• Ensembl ID: ENSPPYG00000007094
• Aliases: None
• Description: trans-golgi network vesicle protein 23 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:20398]

Sequence

>retro_pabe_1344
TTGCAGCAGGATAGTAATGATAACACTAAAGATGTTTCACTGTTTCATGCGGAAGAGGAGACAACTAATAGACCAAGAAA
AGTCAAAATCAGACATCCAGTAGCATCGTTTTTCCACTTATTCTTTCGAGTCAGTGCAATCATCGTCTATTTTCTCTGTG
AGTTGCTCAGTAGCAGCTTTATTACCTGTATGGTAACAATTATCTTGTTGTCATGTGACTTTTGGGCAGTGAAGAATGTC
ACAGGTAGACTAATGGTTGGCCTACGTTGGTGGAATCACATTGATGAAGATGGAAAGAGCCATTGGGTGTTTGAATCTAG
AAAGGAGTCCTCTCAAGAGAATAAAACTGTGTCAGAGGCTGAATCAAGAATCTTTTGGTTGGGACTTATTGCCTGTCCAG
TGCTGTGGGTGATATTTGCCTTTAGTGCACTCTTCTCCTTCAGAGTAAAGTGGTTGGCGGTGGTTTTCATGGATGTGGTG
CTACAAGGTGCCAACCTGTATGGTGACTTCAGGTGTAAGGTGGGCAGCAGAAAGAATTTAACCAGCATGGCTACTTTATA
TTTTGGAAAACAGTTTTTAAGACA

Alignment

ORF - retro_pabe_1344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.84 %
• Parental protein coverage: 91.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKQALVDDTEDVSLDFGNEEELAF-RKAKIRHPLATFFHLFFRVSAIVTYVCCDWFSKSFVGCFVTVLLL
          ..Q...D.T.DVSL....EE.....RK.KIRHP.A.FFHLFFRVSAI..Y..C...S.SF..C.VT..LL
Retrocopy LQQDSNDNTKDVSLFHAEEETTNRPRKVKIRHPVASFFHLFFRVSAIIVYFLCELLSSSFITCMVTIILL

Parental  LSLDFWSVKNVTGRLLVGLRWWNQIDEDGKSHWIFEARKVSPN-SIAATEAEARIFWLGLIICPMIWIVF
          .S.DFW.VKNVTGRL.VGLRWWN.IDEDGKSHW.FE.RK.S........EAE.RIFWLGLI.CP..W..F
Retrocopy -SCDFWAVKNVTGRLMVGLRWWNHIDEDGKSHWVFESRKESSQENKTVSEAESRIFWLGLIACPVLWVIF

Parental  FFSTLFSLKLKWLALVVAGISLQAANLYGYILCKMGGNSDISKVTASFLS-QTVFQT
          .FS.LFS...KWLA.V.....LQ.ANLYG...CK.G................TVF.T
Retrocopy AFSALFSFRVKWLAVVFMDVVLQGANLYGDFRCKVGSRKNLTSMATLYFG<KTVFKT

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	1.05 RPM	20.51 RPM
SRP007412_cerebellum	0.61 RPM	9.97 RPM
SRP007412_heart	1.66 RPM	0.21 RPM
SRP007412_kidney	1.72 RPM	0.20 RPM
SRP007412_liver	2.85 RPM	0.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1344 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1344 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1344 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1625

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015782	2 retrocopies	retro_dord_528, retro_dord_565,
Nomascus leucogenys	ENSNLEG00000010137	1 retrocopy	retro_nleu_2447,
Pongo abelii	ENSPPYG00000007094	1 retrocopy	retro_pabe_1344 ,
Tursiops truncatus	ENSTTRG00000015641	1 retrocopy	retro_ttru_1286,