RetrogeneDB ID: retro_cpor_1282

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_64:5113290..5114634(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATL2
• Ensembl ID: ENSCPOG00000013597
• Aliases: None
• Description: None

Sequence

>retro_cpor_1282
ATAAAGAAACCATGTCCAGTACAAATTGTTCTTGCTCATGAAGATGCTCATAACTTTGAGCTTGATGAAGAAGCCTTGGA
GCAGATTTTGCTACAAGAGCACATACACGACCTTAACATAGTTGTGGTGTCCGTGGCAGGAGCTTTTCGTAAAGGAAAAT
CATTTCTACTGGACTTCATGCTTAGATATATGTATAACAAGGATTCTCAAAGTTGGATTGGCGGAAACAATGAACCATTG
ACTGGCTTTACGTGGAGAGGTGGTTGTGAAAGAGAAACAACGGGCATACAAGTTTGGAATGAAGTATTTGTGATTGACAG
ACCTAATGGAACAAAAGTGGCTGTGCTGCTAATGGATACCCAGGGTGCCTTTGATAGCCAGTCAACTATCAAAGACTGTG
CCACAGTTTTTGCTCTGAGCACTATGACTAGTTCTGTCCAGGTATATAATTTGTCTCAGAATATTCAAGAAGATGATCTT
CAACACTTACAATTATTTACAGAATATGGAAGACTTGCCATGGAAGAAATCTATCAGAAACCATTTCAGACATTAATGTT
TTCGATAAGAGATTGGAGTTATTCTTATGAACATTCATATGGTTTGGAAAGTGGAAAACTTTCTTGAAAAGAGGTTGCAG
GTAAAGCAGAATCAACATGAAGAGCTACAGAATGTAAGGAAGCACATTCATAATTGTTCTCAAATCTGGGTTGCTTCCTT
TTGCCACATCCTGGTCTTAAAGTTGCAACTAATCCTAGCTTTGATGGACGATTGAAAGATATTGATGAAGAATTTAAACG
AGAGCTTCGAAATCTAGTTCCATTGCTGCTTGCCCCTGAAAATTTGGTAAAAAAAGAGATAAGTGGATCTAAAGTCACTT
GTAGAGATCTTGTAGAATATTTTAAGGCTTACATTTAAATTTATCAAGGAGAAGAACTTCCACATCCAAAGTCCATGCTT
CAGGCAACAGCTGAAGCTAATAATCTTGCTGCAGTAGCAGGAGCATGAGATATCTATTGCAAAAGTATGGAACAGGTATG
TGGTGGGGACAAGCCTTACATTGCACCTTCAGACCTGGAACGAAAACACCTGGATCTCAAGGAAGTGGCAATTAGTCAGT
TTTGTTCTGTGAAAAAAATGGGTGGAGATGAGTTCTGCTGTCGTTATCAGGACCAGCTTGAAGCTGAAATTGAAGAAACC
TATGCAAATTTTATAAAGCACAATGATGGCAAAAATATTTTTTATGCTGCTCGTACCCCTGCCATGCTGTTTGCGGTTAT
GTTTGCAATGTATATAATCTCAGGACTGACTGGCTTCATTGGCCTGAACTCTTGTGTAACCTTG

Alignment

ORF - retro_cpor_1282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.91 %
• Parental protein coverage: 84.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKKPCPVQIVLAHEDDHNFELDEEALEQILLQEHIRDLNIVVVSVAGAFRKGKSFLLDFMLRYMYNKDSQ
          .KKPCPVQIVLAHED.HNFELDEEALEQILLQEHI.DLNIVVVSVAGAFRKGKSFLLDFMLRYMYNKDSQ
Retrocopy IKKPCPVQIVLAHEDAHNFELDEEALEQILLQEHIHDLNIVVVSVAGAFRKGKSFLLDFMLRYMYNKDSQ

Parental  SWIGGNNEPLTGFTWRGGCERETTGIQVWNEVFVIDRPNGTKVAVLLMDTQGAFDSQSTIKDCATVFALS
          SWIGGNNEPLTGFTWRGGCERETTGIQVWNEVFVIDRPNGTKVAVLLMDTQGAFDSQSTIKDCATVFALS
Retrocopy SWIGGNNEPLTGFTWRGGCERETTGIQVWNEVFVIDRPNGTKVAVLLMDTQGAFDSQSTIKDCATVFALS

Parental  TMTSSVQVYNLSQNIQEDDLQHLQLFTEYGRLAMEEIYQKPFQVTLFGIRDWSYPYEHSYGLEGG-KQFL
          TMTSSVQVYNLSQNIQEDDLQHLQLFTEYGRLAMEEIYQKPFQ...F.IRDWSY.YEHSYGLE.G.K.FL
Retrocopy TMTSSVQVYNLSQNIQEDDLQHLQLFTEYGRLAMEEIYQKPFQTLMFSIRDWSYSYEHSYGLESG<KTFL

Parental  E-KRLQVKQNQHEELQNVRKHIHNC-FSNLGCFLLPHPGLKVATNPSFDGRLKDIDEEFKRELRNLVPLL
          ..KRLQVKQNQHEELQNVRKHIHNC.FSNLGCFLLPHPGLKVATNPSFDGRLKDIDEEFKRELRNLVPLL
Retrocopy K<KRLQVKQNQHEELQNVRKHIHNC<FSNLGCFLLPHPGLKVATNPSFDGRLKDIDEEFKRELRNLVPLL

Parental  LAPENLVEKEISGSKVTCRDLVEYFKAYIKIYQGEELPHPKSMLQATAEANNLAAVAGARDIYCKSMEQV
          LAPENLV.KEISGSKVTCRDLVEYFKAYI.IYQGEELPHPKSMLQATAEANNLAAVAGA.DIYCKSMEQV
Retrocopy LAPENLVKKEISGSKVTCRDLVEYFKAYI*IYQGEELPHPKSMLQATAEANNLAAVAGA*DIYCKSMEQV

Parental  CGGDKPYIAPSDLERKHLDLKEVAIRQFCSVKKMGGDEFCRRYQDQLEAEIEETYANFIKHNDGKNIFYA
          CGGDKPYIAPSDLERKHLDLKEVAI.QFCSVKKMGGDEFC.RYQDQLEAEIEETYANFIKHNDGKNIFYA
Retrocopy CGGDKPYIAPSDLERKHLDLKEVAISQFCSVKKMGGDEFCCRYQDQLEAEIEETYANFIKHNDGKNIFYA

Parental  ARTPATLFAVMFAMYIISGLTGFIGLNSIAVL
          ARTPA.LFAVMFAMYIISGLTGFIGLNS...L
Retrocopy ARTPAMLFAVMFAMYIISGLTGFIGLNSCVTL

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	1.15 RPM	23.52 RPM
SRP017611_kidney	0.73 RPM	26.80 RPM
SRP017611_liver	2.61 RPM	65.94 RPM
SRP040447_lung	0.58 RPM	41.89 RPM
SRP040447_skeletal_muscle	0.72 RPM	38.72 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1282 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1282 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.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013597	1 retrocopy	retro_cpor_1282 ,
Tupaia belangeri	ENSTBEG00000002649	1 retrocopy	retro_tbel_3220,