RetrogeneDB ID: retro_pabe_132

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:37633227..37634451(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020233
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TFDP1
• Ensembl ID: ENSPPYG00000025889
• Aliases: None
• Description: transcription factor Dp-1 [Source:HGNC Symbol;Acc:11749]

Sequence

>retro_pabe_132
ATGGCAAAAGATGCCGGTCTAATTGAAGCCAACGGAGAACTCAAGGTCTTCATAGACCAGAACCTTAGTTCCGGAAAAGG
CGTGGTGTCCCTCGTGGCCGTTCACCCCTCCACCGTCAATCCGCTCGGGAAACAGCTCTTGCCAAAAACCTTTGGACAGT
CCAATGTCAGCATTGCCCAGCAAGTGGTGATTGGTATGCCTCAGAGACCTGCAGCGTCAAACACCCTGGTGGTAGGAAGC
TCACACACCCCCAGCACTCACTTTGCCTCTCAGAACCAGCCTTCTGATTCCTCACCTCGGTCTGCAGGGAAGCGCAACAG
GAAAGGAGAGAATTGCAAGGGCCTGCGGCATTTCTCCATGAAGGTCTGCGAGAAGGTGCAGAGGAAAGGGACCACTTCCT
ACAACGAAGTGGCAGACGAGCTGGTCGCGGAGTTCAGTGCTGCCGACAACCACATCTTACCAAACGAGTCAGCTTATGAC
CAGAAGAACATAAGACGGCGCGTCTATGATGCCTTAAACGTGCTGATGGCCATGAACATCATCTCCAAGGAGAAGAAGGA
GATTAAGTGGATTGGTCTGCCCACCAGCTCGGCTCAGGAATGTCAGAACTTAGAGGTGGAAAGACAGAGGAGACTTGAAA
GAATAAAACAGAAACAGTCTCAACTTCAAGAACTTATTCTACAGCAAATTGCCTTCAAGAACCTGGTGCAGAGAAACCGG
CACGCAGAGCAGCAGGCCAGCCGGCCGCCACCACCCAACTCGGTCATCCACCTGCCCTTCATCGTCGTCAACACCAGCAA
GAAGACCGTCATCAACTGCAGCATCTCCAACGACAAACTGGAGTATCTGTTTAATTTTGACAACACATTTGAAATCCAAG
GTGACATAGAAGTGCTGAAGCGGATGGGCATGGCTTGCTGGCTGGAGTCCGGGAGCTGCTCTGCTGAAGACCTTAAAATG
GCCAGAAGTCTAGTCCCAAAGGCGCTGGAGCCGTATGTGACAGAAATGGCTCAGGGAACTGTTGGAGGCAAGTTCATCAC
GGCGGCAGGTTCCACGTCTAAAGGCACGAGGTTCTCTGCCAGTGACCTGACCAACGGTGCAGATGGGATGCTGGCCACAA
GCTCCAAGAGGTCTCAGTACAGCGGCTCCAGGGTGGAGACCCCGGTGTCCTACGTCGGGGAGGACGAGGAGGATGATGAC
TTCAACGAGAATGACAAGGACGAC

Alignment

ORF - retro_pabe_132 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKDAGLIEANGELKVFIDQNLSPGKGVVSLVAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQRP
          MAKDAGLIEANGELKVFIDQNLS.GKGVVSLVAVHPSTVNPLGKQLLPKTFGQSNV.IAQQVVIG.PQRP
Retrocopy MAKDAGLIEANGELKVFIDQNLSSGKGVVSLVAVHPSTVNPLGKQLLPKTFGQSNVSIAQQVVIGMPQRP

Parental  AASNTLVVGSPHTPSTHFASQNQPSDSSPWSAGKRNRKGEKNGKGLRHFSMKVCEKVQRKGTTSYNEVAD
          AASNTLVVGS.HTPSTHFASQNQPSDSSP.SAGKRNRKGE.N.KGLRHFSMKVCEKVQRKGTTSYNEVAD
Retrocopy AASNTLVVGSSHTPSTHFASQNQPSDSSPRSAGKRNRKGE-NCKGLRHFSMKVCEKVQRKGTTSYNEVAD

Parental  ELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVERQ
          ELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPT.SAQECQNLEVERQ
Retrocopy ELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTSSAQECQNLEVERQ

Parental  RRLERIKQKQSQLQELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISNDK
          RRLERIKQKQSQLQELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFI.VNTSKKTVI.CSISNDK
Retrocopy RRLERIKQKQSQLQELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIVVNTSKKTVINCSISNDK

Parental  FEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGVFITTA
          .EYLFNFDNTFEI..DIEVLKRMGMAC.LESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGG.FIT.A
Retrocopy LEYLFNFDNTFEIQGDIEVLKRMGMACWLESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGKFITAA

Parental  GSTSNGTRFSASDLTNGADGMLATSSNGSQYSGSRVETPVSYVGEDDEEDDDFNENDEDD
          GSTS.GTRFSASDLTNGADGMLATSS..SQYSGSRVETPVSYVGE.DEEDDDFNEND.DD
Retrocopy GSTSKGTRFSASDLTNGADGMLATSSKRSQYSGSRVETPVSYVGE-DEEDDDFNENDKDD

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	0.66 RPM	20.68 RPM
SRP007412_cerebellum	0.12 RPM	34.05 RPM
SRP007412_heart	0.09 RPM	16.50 RPM
SRP007412_kidney	0.10 RPM	21.74 RPM
SRP007412_liver	0.24 RPM	11.23 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_132 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_132 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_132 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_17

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229, retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243, retro_mmus_338,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314, retro_pabe_132 , retro_pabe_378,