RetrogeneDB ID: retro_ptro_1933

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:150235572..150236874(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAP2C
• Ensembl ID: ENSPTRG00000013654
• Aliases: None
• Description: transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) [Source:HGNC Symbol;Acc:11744]

Sequence

>retro_ptro_1933
GATCGCCACAACGGGAGCAGCAATGGGAATCCGCGAGTCCCCCACCTCTCCTCCGCCGGGCAGCACCTCTACAGCCCCGC
GCCACCCCTCTCCCACACTGGAGTCGCCGAGTATCAGCCGCCACCCTACTTTCCCCCTCCCTACCAGCAGCTGGCCTACT
CCCAGTCGGCCGACCCCTACTCGCATCTGGGGGAAGCGTACGCCGCCGCCATCAACCCCCTGCACCAGCCGGCGCCCACA
GGCAGCCAGCAGCAGGCCTGGCCCGGCCGCCAGAGCCAGGAGGGAGCGGGGCTGCCCTCGCACCACGGGCGCCCGGCCGG
CCTGCTGCCCCACCTCTCCGGGCTGGAGGCGGGCGCGGTGAGCGCCGGCAGGGATGCCCACCGCCGCTCCGACCTGCTGC
TGCCACACGCACACGCCCTGGATGCCGCGGGCCTGGCCGAGAACCTGGGGCTCCACGACATGCCTCACTAGATGGACGAG
GTGCAGAATGTCGACGACCAGCACCTGTTGCTGCACGATCAGACAGTCATTCGCAAAGGTCCCATTTCCATGACCAAGAA
CTCTCTGAACCTCCCCTGTCAGAAGGAGCTGGTGGGGGCCGTAATGAACCCCACTGAGGTCTTCCGCTCAGTCCCTGGAA
GATTGTCGCTCCTCAGCTCTACGTCTAAATACAAAGTGACAGTGGCTGAAGTACAGAGGCGACTGTCCCCACCTGAATGC
TTAAATGCCTCGTTACTGGGAGGTGTTCTGAGAAGAGCCAAATCGAAAAATGGAGGCCGGTCCTTGCGGGAGAAGTTGGA
CAAGGTTGGGTTGAATCTTCCGGCTGGGAGACGGAAAGCCGCTCATGTGACTCTCCTGACATCCTTAGTAGAAGGTGAAG
CTGTTCATTTGGCTAGGGACTTTGCCTATATCTGTGAAGCCGAATTTCCTGGTAAACCAGTGGCAGAATACTTAACCAGA
CCTCATCTTGGAGGACGAAATGAGATGGCAGCTAGGAAGAACATGCTATTGGCGGCCCAGCAACTGTGTAAAGAATTCAC
AGAACTTCTCAGCCAAGACCGGACACCCCATGGGACCAGCAGGCTCGCCCCAGTCTTGGAGACGAACATACAGAACTGCT
TGTCTCATTTCAGCCTGATTACCCACGGGTTTGGCAGCCAGGCCATCTGTGCCGCGGTGTCTGCCCTGCAGAACTACATC
AAAGAAGCCCTGATTGTCATAGACAAATCCTACATGAACCCTGGAGACCAGAGTCCAGCTGATTCTAACAAAACCCTGGA
GAAAATGGAGAAGCACAGGAAA

Alignment

ORF - retro_ptro_1933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.93 %
• Parental protein coverage: 96.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRHDGSSNGNPRVPHLSSAGQHLYSPAPPLSHTGVAEYQPPPYFPPPYQQLAYSQSADPYSHLGEAYAAA
          DRH.GSSNGNPRVPHLSSAGQHLYSPAPPLSHTGVAEYQPPPYFPPPYQQLAYSQSADPYSHLGEAYAAA
Retrocopy DRHNGSSNGNPRVPHLSSAGQHLYSPAPPLSHTGVAEYQPPPYFPPPYQQLAYSQSADPYSHLGEAYAAA

Parental  INPLHQPAPTGSQQQAWPGRQSQEGAGLPSHHGRPAGLLPHLSGLEAGAVSARRDAYRRSDLLLPHAHAL
          INPLHQPAPTGSQQQAWPGRQSQEGAGLPSHHGRPAGLLPHLSGLEAGAVSA.RDA.RRSDLLLPHAHAL
Retrocopy INPLHQPAPTGSQQQAWPGRQSQEGAGLPSHHGRPAGLLPHLSGLEAGAVSAGRDAHRRSDLLLPHAHAL

Parental  DAAGLAENLGLHDMPHQMDEVQNVDDQHLLLHDQTVIRKGPISMTKNPLNLPCQKELVGAVMNPTEVFCS
          DAAGLAENLGLHDMPH.MDEVQNVDDQHLLLHDQTVIRKGPISMTKN.LNLPCQKELVGAVMNPTEVF.S
Retrocopy DAAGLAENLGLHDMPH*MDEVQNVDDQHLLLHDQTVIRKGPISMTKNSLNLPCQKELVGAVMNPTEVFRS

Parental  VPGRLSLLSSTSKYKVTVAEVQRRLSPPECLNASLLGGVLRRAKSKNGGRSLREKLDKIGLNLPAGRRKA
          VPGRLSLLSSTSKYKVTVAEVQRRLSPPECLNASLLGGVLRRAKSKNGGRSLREKLDK.GLNLPAGRRKA
Retrocopy VPGRLSLLSSTSKYKVTVAEVQRRLSPPECLNASLLGGVLRRAKSKNGGRSLREKLDKVGLNLPAGRRKA

Parental  AHVTLLTSLVEGEAVHLARDFAYVCEAEFPSKPVAEYLTRPHLGGRNEMAARKNMLLAAQQLCKEFTELL
          AHVTLLTSLVEGEAVHLARDFAY.CEAEFP.KPVAEYLTRPHLGGRNEMAARKNMLLAAQQLCKEFTELL
Retrocopy AHVTLLTSLVEGEAVHLARDFAYICEAEFPGKPVAEYLTRPHLGGRNEMAARKNMLLAAQQLCKEFTELL

Parental  SQDRTPHGTSRLAPVLETNIQNCLSHFSLITHGFGSQAICAAVSALQNYIKEALIVIDKSYMNPGDQSPA
          SQDRTPHGTSRLAPVLETNIQNCLSHFSLITHGFGSQAICAAVSALQNYIKEALIVIDKSYMNPGDQSPA
Retrocopy SQDRTPHGTSRLAPVLETNIQNCLSHFSLITHGFGSQAICAAVSALQNYIKEALIVIDKSYMNPGDQSPA

Parental  DSNKTLEKMEKHRK
          DSNKTLEKMEKHRK
Retrocopy DSNKTLEKMEKHRK

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	0.02 RPM	0.20 RPM
SRP007412_cerebellum	0.11 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.09 RPM
SRP007412_kidney	0.00 RPM	0.21 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1933 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1933 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011025	1 retrocopy	retro_chof_1226,
Macropus eugenii	ENSMEUG00000007703	1 retrocopy	retro_meug_166,
Myotis lucifugus	ENSMLUG00000010003	2 retrocopies	retro_mluc_284, retro_mluc_5,
Monodelphis domestica	ENSMODG00000016445	1 retrocopy	retro_mdom_728,
Otolemur garnettii	ENSOGAG00000033901	1 retrocopy	retro_ogar_1767,
Pan troglodytes	ENSPTRG00000013654	1 retrocopy	retro_ptro_1933 ,
Ictidomys tridecemlineatus	ENSSTOG00000014299	3 retrocopies	retro_itri_1741, retro_itri_1801, retro_itri_1813,
Tursiops truncatus	ENSTTRG00000005983	1 retrocopy	retro_ttru_535,