RetrogeneDB ID: retro_ptro_1300

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:56111739..56112727(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDCCAG3
• Ensembl ID: ENSPTRG00000021555
• Aliases: None
• Description: Serologically defined colon cancer antigen 3 [Source:UniProtKB/TrEMBL;Acc:K7BM14]

Sequence

>retro_ptro_1300
GATTTGGGCTATGGAAAGGGGAAATGTTCTAAGCAGAGCCCGTCAGGAGCCCACGAGACACATTTTGGAGATGACAAATT
TGAAGATCTTGAAGAGGCAAATCCATTCTCCTTTAAAGAGTTTCTGAAGACCAAGAACCTCGGCCTGTCAAAAGAGGACC
CGGCCAGCAGAATTTATGCAAAGGAAGCGTCGAGGTATTCACTGGGACTTGACCACAACTCCCCACTCTCCCAAACCGGG
GGGTATGGCCTGGAGTATCAGCAGCCATTTTTCGAGGACCCGACAGGGGCCGGTGACCTCCTGGATGAGGAGGAGGATGA
GACACCGGATGGAGTGGGGCCTACCTGCCGTCCGCCATCCAGCAGACTCACCCGGAGAGGGTCCCTGCCTGCACGTTGCC
CTGCAGCACATACCTTTCCTTTTTCTCCACCCCATCAGAGCTGGCAGGGCCCGAGTCTCTGCTCCCGTCGGCGTTGAGTG
ACACTGATTCTCACGTGTCTCCGGCCTCTCCGGCAGGGAGTCCTAGCACAGATTTTGCGGCTCATGGAGAGTCTCTGGGA
GACAGGCACCTGCGGACGCTGCAGATAAGTTACGAAGCACTGAAAGATGAAAATTCTAAGCTGAGAAGAAAGCTGAATGA
GGTTCAGAGCTTCTCTGAAGCTCAAACAGAAATGGTGAGGACACTTGTGCAGAAATTAGAAGCAAAAATGATCAACGAGG
AAAGCGACTACCACGACTTAGAGTTGATGGTTCAGCAGGTGGAGCAGAACCTGGAGCTGATGACCAAACGGGCTGTAAAG
GCAGAAAACCATGTCGTGAAACTGAACAGGAAATCAGTTTGCTGCAGGCGCAGGTCTCCAGCTTCCAGCGAGAGAATGAA
GCCCTGCGGTGCGACCAGGGGGCCAGCCTGACAGTGGTGAAGCAGAATGCCGACGTGGCCTTGCAGAACCTCTGGGTGGT
CATGAACAGAGCACAGGCTTCCATTAAG

Alignment

ORF - retro_ptro_1300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.87 %
• Parental protein coverage: 81.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DFGYGKGKCSKQSPSGAHGTHFGDDRFEDLEEANPFSFKEFLKTKNLGLSKEDPASRIYAKEASRHSLGL
          D.GYGKGKCSKQSPSGAH.THFGDD.FEDLEEANPFSFKEFLKTKNLGLSKEDPASRIYAKEASR.SLGL
Retrocopy DLGYGKGKCSKQSPSGAHETHFGDDKFEDLEEANPFSFKEFLKTKNLGLSKEDPASRIYAKEASRYSLGL

Parental  DHNSPPSQTGGYGLEYQQPFFEDPTGAGDLLDEEEDE-DTGWSGAYLPSAIEQTHPERVPAGTSPCSTYL
          DHNSP.SQTGGYGLEYQQPFFEDPTGAGDLLDEEEDE.DTGWSGAYLPSAI.QTHPERVPA.T.PCSTYL
Retrocopy DHNSPLSQTGGYGLEYQQPFFEDPTGAGDLLDEEEDE<DTGWSGAYLPSAIQQTHPERVPACTLPCSTYL

Parental  SFFSTPSELAGPESLPSWALSDTDSRVSPASPAGSPSADFAVHGESLGDRHLRTLQISYDALKDENSKLR
          SFFSTPSELAGPESL...ALSDTDS.VSPASPAGSPS.DFA.HGESLGDRHLRTLQISY.ALKDENSKLR
Retrocopy SFFSTPSELAGPESLLPSALSDTDSHVSPASPAGSPSTDFAAHGESLGDRHLRTLQISYEALKDENSKLR

Parental  RKLNEVQSFSEAQTEMVRTLERKLEAKMIKEESDYHDLESVVQQVEQNLELMTKRAVKAENHVVKL-KQE
          RKLNEVQSFSEAQTEMVRTL..KLEAKMI.EESDYHDLE..VQQVEQNLELMTKRAVKAENHVVKL..QE
Retrocopy RKLNEVQSFSEAQTEMVRTLVQKLEAKMINEESDYHDLELMVQQVEQNLELMTKRAVKAENHVVKL<EQE

Parental  ISLLQAQVSNFQRENEALRCGQGASLTVVKQNADVALQNLRVVMNSAQASIK
          ISLLQAQVS.FQRENEALRC.QGASLTVVKQNADVALQNL.VVMN.AQASIK
Retrocopy ISLLQAQVSSFQRENEALRCDQGASLTVVKQNADVALQNLWVVMNRAQASIK

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	0.13 RPM	9.85 RPM
SRP007412_cerebellum	0.39 RPM	9.82 RPM
SRP007412_heart	0.20 RPM	5.04 RPM
SRP007412_kidney	0.58 RPM	19.61 RPM
SRP007412_liver	0.62 RPM	28.77 RPM
SRP007412_testis	1.69 RPM	46.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1300 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1300 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1944
Gorilla gorilla	retro_ggor_1414

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000165689	1 retrocopy	retro_hsap_1944,
Gorilla gorilla	ENSGGOG00000010905	1 retrocopy	retro_ggor_1414,
Mus musculus	ENSMUSG00000026927	3 retrocopies	retro_mmus_1545, retro_mmus_3492, retro_mmus_711,
Nomascus leucogenys	ENSNLEG00000008186	1 retrocopy	retro_nleu_891,
Otolemur garnettii	ENSOGAG00000015872	1 retrocopy	retro_ogar_3418,
Pongo abelii	ENSPPYG00000019772	2 retrocopies	retro_pabe_1612, retro_pabe_256,
Pan troglodytes	ENSPTRG00000021555	1 retrocopy	retro_ptro_1300 ,
Rattus norvegicus	ENSRNOG00000018876	2 retrocopies	retro_rnor_1215, retro_rnor_2770,