RetrogeneDB ID: retro_pabe_983

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:22005147..22005767(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB14
• Ensembl ID: ENSPPYG00000014956
• Aliases: None
• Description: dnaJ homolog subfamily B member 14 [Source:RefSeq peptide;Acc:NP_001126547]

Sequence

>retro_pabe_983
TTGAAGTTTCATCCAGACAAACACCATGCACCTGGAGAAACAGATGCTTTTAAAAAGTTTGGAAATGCTTATGCTGTTTT
AAATAATCCAGAAAGCGAAAACGGTATGACCTCACAGGCAATGAAGAGCAAGCATGTAACCACCAAAATAATGGCAGATT
TAATTTCCATAGAGGTTGTGAAGCTGATATAACTCCAGAAGAGTTGTTTAATATACTTTTTGGGGGTGGATTTACTTCGG
GTAATATACATTCTTTTTCAAATGGACGAGCTCGTGATAGCCAACAACATCAGCATCGACATAGGCGACATGAAAGAGAA
GAGGAAAGAGGAGATGGAGGTTTTTCTGTGTTTATCCAGCTGATGCCCATAATTGTATTGATCCTCGTGTCATTATTAAG
CCAACTGATGGTCTCTAATCCTCCTTACTCCTTATATCCCAGATCTGGAACAGGGCAAACTATTAAAATGCAGACAGAAA
ACTTGGTTGTTGTTTATTACGTCAACAAGGACTTTAAAAACGAATATAAAGGAATGTTATTACAAAAGGTAGAAAAGAGT
GTGGAAGAAGATTATGTGACTAATATTCGAAATAATTGCTGGAAAGACAACAAAAAACAG

Alignment

ORF - retro_pabe_983 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.9 %
• Parental protein coverage: 62.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKFHPDKNHAPGATDAFKKIGNAYAVLSNPE-KRKQYDLTGNEEQACNHQNNGRFNFHRGCEADITPEDL
          LKFHPDK.HAPG.TDAFKK.GNAYAVL.NPE.KRK.YDLTGNEEQACNHQNNGRFNFHRGCEADITPE.L
Retrocopy LKFHPDKHHAPGETDAFKKFGNAYAVLNNPE<KRKRYDLTGNEEQACNHQNNGRFNFHRGCEADITPEEL

Parental  FNIFFGGGFPSGSVHSFSNGRAGYSQQHQHRHSGHEREEERGDGGFSVFIQLMPIIVLILVSLLSQLMVS
          FNI.FGGGF.SG..HSFSNGRA..SQQHQHRH..HEREEERGDGGFSVFIQLMPIIVLILVSLLSQLMVS
Retrocopy FNILFGGGFTSGNIHSFSNGRARDSQQHQHRHRRHEREEERGDGGFSVFIQLMPIIVLILVSLLSQLMVS

Parental  NPPYSLYPRSGTGQTIKMQTENLGVVYYVNKDFKNEYKGMLLQKVEKSVEEDYVTNIRNNCWKERQQK
          NPPYSLYPRSGTGQTIKMQTENL.VVYYVNKDFKNEYKGMLLQKVEKSVEEDYVTNIRNNCWK.....
Retrocopy NPPYSLYPRSGTGQTIKMQTENLVVVYYVNKDFKNEYKGMLLQKVEKSVEEDYVTNIRNNCWKDNKKQ

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	0.00 RPM	10.51 RPM
SRP007412_cerebellum	0.00 RPM	9.97 RPM
SRP007412_heart	0.00 RPM	2.74 RPM
SRP007412_kidney	0.00 RPM	4.41 RPM
SRP007412_liver	0.00 RPM	2.48 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_983 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_983 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_983 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012468	1 retrocopy	retro_acar_144,
Homo sapiens	ENSG00000164031	1 retrocopy	retro_hsap_1583,
Monodelphis domestica	ENSMODG00000020687	2 retrocopies	retro_mdom_1398, retro_mdom_752,
Nomascus leucogenys	ENSNLEG00000013668	2 retrocopies	retro_nleu_1761, retro_nleu_2409,
Otolemur garnettii	ENSOGAG00000005340	1 retrocopy	retro_ogar_120,
Pongo abelii	ENSPPYG00000002353	1 retrocopy	retro_pabe_1945,
Pongo abelii	ENSPPYG00000014956	3 retrocopies	retro_pabe_1304, retro_pabe_982, retro_pabe_983 ,
Pan troglodytes	ENSPTRG00000016311	1 retrocopy	retro_ptro_1066,
Ictidomys tridecemlineatus	ENSSTOG00000021338	1 retrocopy	retro_itri_1840,