RetrogeneDB ID: retro_cpor_1533

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_95:1287918..1288775(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000023395
• Aliases: None
• Description: None

Sequence

>retro_cpor_1533
AAGGTTATCTTTGGCTCATTTTAATCTACACTGACTGTAAATGGATAATTTTCTTTGCTCTATCAGGTGGCCCCAAAGGA
CACATATTTGGTCATTGGAAAGGTGTCCTTGATGCTTCATTTCTACTGGACGTGGGTGGGGCTGCTCATTACAGAAGGCC
ATAAGGGTCTTCAGTTTCTCTCAGATGTGAGAACTGAGATTAATAAGAACCGAATTTGGATAGCCTTTGTAAAATGATCT
CAACTATGACTGTGTCATATCTCTCAGGCATACAGAATCATAGTATCCTGCCTGCAGATACATCTTCAGTCAATGTAGTG
GTTATTTACTATGACAGTGATAATCCAAGTGATGTGAGATACATATAGTGCAACATTTAGAGTCATGGAAAATCTGGATA
ACAAACTCACAATGGCAAGCTGACATGGATGGATGAAATTTCATACATGATCCATTCCATGTTCTTACTTTTTCACACCA
GCATGAAGAGATTTTAAATTTTAAAACTTTTGTACAAAAGCTACCACATTTAAATACTCTGAAGACAATTTTTTGTTATG
TATCAATACAAGTATTTCTGTTGCTCCTTCTCTGAATCTGACTGTGCACTGGAGAACTGTACACCTAATGCCTCTCTGGC
TTGGCTGCCTCCAAATAGTTTTGACACAACCATGAGTGATAGAAGCTACAATATACACAATGATGTGTATGCTGTGGCCT
ATACCTTCCAGGTGATGCTTTCTGAAGAAGTACAAAGCCCTTAAATGAGAAATAGACAAGATGATGTTTCCCCCTCGCAG
GTAATACGTGTTCTTTTGGATGGCATGCAGTGTCACCAATGTGCCTCAGTCCAATTG

Alignment

ORF - retro_cpor_1533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.12 %
• Parental protein coverage: 56.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QVYYGLFDPTLSESGQYPLLHQVAQKDTFLALAMVSLMLHFHWTWVGLLTTEGHKGLQFLSDVRTEMDRN
          .V..G.F..TL...G...LL.QVA.KDT.L....VSLMLHF.WTWVGLL.TEGHKGLQFLSDVRTE...N
Retrocopy KVIFGSF*STLTVNG*FSLLYQVAPKDTYLVIGKVSLMLHFYWTWVGLLITEGHKGLQFLSDVRTEINKN

Parental  RVCVAFVK-IVASSTVLYFSAMQKHDILTADTSSVNVVVIYYDTNSIHDVSY-HIVQNLMTWKIWVTNSQ
          R...AFVK......TV.Y.S..Q.H.IL.ADTSSVNVVVIYYD.....DV.Y.HIVQ.L..WKIW.TNSQ
Retrocopy RIWIAFVK<MISTMTVSYLSGIQNHSILPADTSSVNVVVIYYDSDNPSDVRY<HIVQHLESWKIWITNSQ

Parental  WQADLDGRNFILDSFHGVLVFSHHYEEISGFKNYVQE-ATPFKYPDDTYLF-MYWYKNFHCSFSESDCTL
          WQAD.DG.NFI.D.FH.VL.FSH..EEI..FK..VQ..AT.FKY..D..L..MY.YK.F.CSFSESDC.L
Retrocopy WQADMDG*NFIHDPFH-VLTFSHQHEEILNFKTFVQK<ATTFKYSEDNFLL<MYQYKYFCCSFSESDCAL

Parental  ENCTPNASLAWLPPNHFDTAMNDRSYNIYNGVYAVAHALHAMLFAEEQGPSMRNRQMKMFSPWQQLNPFL
          ENCTPNASLAWLPPN.FDT.M.DRSYNI.N.VYAVA.....ML..E.Q.P.MRNRQ....SP.Q.....L
Retrocopy ENCTPNASLAWLPPNSFDTTMSDRSYNIHNDVYAVAYTFQVMLSEEVQSP*MRNRQDDV-SPSQVIRVLL

Parental  KNIQFSNSAGDQV
          ...Q....A..Q.
Retrocopy DGMQCHQCASVQL

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	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.00 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1533 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1533 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023395	2 retrocopies	retro_cpor_1533 , retro_cpor_1534,