RetrogeneDB ID: retro_cpor_1369

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_73:5809333..5810412(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000004176
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAOA
• Ensembl ID: ENSCPOG00000001030
• Aliases: None
• Description: None

Sequence

>retro_cpor_1369
AGACTGCTAAAGCAGTTTGCTACTCTATTGTGAATATCAATGTGACCTCTGAGCCCCATGAGGTCTCTGCTCTGTGGTTT
CTGTGGTATGTGAAGCAATGTGGTGGTACCTCTCGGATATTCTCAATCACCAATGGAGGCCAGGAACGGAAGTTTAAGGG
TGGATCTGGTCAAGTGAGTGAAAGAATAATGGGCCTCCTAGGTGACCGAGTGAAGCTGAACTGCCCTGTCACCTATGTTG
ACCAGTCAGGTGGCAACATCATTATAGAGACACTGAATCATGAACGCTATGAGTGCAGATATGTGATTAGCGCCATCCCT
CCAACTTTAACTGCCAAGATCCACTTCAGACCAGAACTTCCACCAGAGAGAACCCAGTTAATCCAGCGCCTTCCAATGGG
GTCTGTCATTAAGTGCATGATGTATTATAGGGAAGCCTTCTGGAAGAAAAAGGATTACTGTGGCTGCATGATCATTGAGG
ATGAAGAAGCCCCAATTTCCATTACCCTGGATGACACCAAACCAGATGAATCAGTGCCCGCCATCATGGGCTTCATACTT
GCCCGGAAAGCTGATCGGCTTGCTAAACTCCATAAGGAAATAAGGAAGAAGAAAATCTGTGAACTGTATGCCAAAGTGCT
GGGATCTCAAGAAGCTTTAGAGCCCGTGCATTATGAAGAGAAGAACTGGTGTGAGGAGCAATACTCTGGGGGCTGCTACA
CAGCCTACTTCCCTCCCGGGATCATGACCCAGTATGGAAGAGTGATTCGCCAGCCAGTGGGCAGGATTTACTTTGCTGGC
ACAGAGACTGCCACACAGTGGAGCGGGTACATGGAGGGAGCAGTTGAGGCTGGAGAACGGGCAGCTAGAGAGGTTTTAAA
TGCTCTTGGGAAGGTGGCCAAGGAGGATATATGGGTGCAAGAACCTGAGTGCAAGGATGTTCCATCAGTTGAGATCACCC
GTACCTTCTTGGAGAGGAACCTGCCTTCTGTGCCTGGCCTCCTGAAGATTATTGGAATATCAACCTCGCTAACTGCCTTC
GGGTTTGTGTTGCAAAAGTACAAGCTACTGCCACAGTCC

Alignment

ORF - retro_cpor_1369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.98 %
• Parental protein coverage: 71.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RTAKQFATLF-VNINVTSEPHEVSALWFLWYVKQCGGTSRIFSITNGGQERKFKGGSGQVSERIMGLLGD
          R..KQFATL..VNINVTSEPHEVSALWFLWYVKQCGGTSRIFSITNGGQERKFKGGSGQVSERIMGLLGD
Retrocopy RLLKQFATLL<VNINVTSEPHEVSALWFLWYVKQCGGTSRIFSITNGGQERKFKGGSGQVSERIMGLLGD

Parental  RVKLNCPVTYVDQSGGNIIIETLNHERYECRYVISAIPPTLTAKIHFRPELPPERTQLIQRLPMGSVIKC
          RVKLNCPVTYVDQSGGNIIIETLNHERYECRYVISAIPPTLTAKIHFRPELPPERTQLIQRLPMGSVIKC
Retrocopy RVKLNCPVTYVDQSGGNIIIETLNHERYECRYVISAIPPTLTAKIHFRPELPPERTQLIQRLPMGSVIKC

Parental  MMYYREAFWKKKDYCGCMIIEDEEAPISITLDDTKPDESVPAIMGFILARKADRLAKLHKEIRKKKICEL
          MMYYREAFWKKKDYCGCMIIEDEEAPISITLDDTKPDESVPAIMGFILARKADRLAKLHKEIRKKKICEL
Retrocopy MMYYREAFWKKKDYCGCMIIEDEEAPISITLDDTKPDESVPAIMGFILARKADRLAKLHKEIRKKKICEL

Parental  YAKVLGSESFPHDLQPVHYEEKNWCEEQYSGGCYTAYFPPGIMTQYGRVIRQPVGRIYFAGTETATQWSG
          YAKVLGS......L.PVHYEEKNWCEEQYSGGCYTAYFPPGIMTQYGRVIRQPVGRIYFAGTETATQWSG
Retrocopy YAKVLGSQ---EALEPVHYEEKNWCEEQYSGGCYTAYFPPGIMTQYGRVIRQPVGRIYFAGTETATQWSG

Parental  YMEGAVEAGERAAREVLNALGKVAKEDIWVQEPECKDVPSVEITRTFLERNLPSVPGLLKIIGISTSLTA
          YMEGAVEAGERAAREVLNALGKVAKEDIWVQEPECKDVPSVEITRTFLERNLPSVPGLLKIIGISTSLTA
Retrocopy YMEGAVEAGERAAREVLNALGKVAKEDIWVQEPECKDVPSVEITRTFLERNLPSVPGLLKIIGISTSLTA

Parental  FGFVLQKYKLLPQS
          FGFVLQKYKLLPQS
Retrocopy FGFVLQKYKLLPQS

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
SRP017611_brain	0.23 RPM	10.81 RPM
SRP017611_kidney	5.02 RPM	105.52 RPM
SRP017611_liver	4.96 RPM	114.82 RPM
SRP040447_lung	0.33 RPM	43.41 RPM
SRP040447_skeletal_muscle	0.14 RPM	11.34 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1369 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1369 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001030	1 retrocopy	retro_cpor_1369 ,
Tursiops truncatus	ENSTTRG00000009039	1 retrocopy	retro_ttru_388,