RetrogeneDB ID: retro_cpor_1126

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_49:13724349..13726304(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP85
• Ensembl ID: ENSCPOG00000001185
• Aliases: None
• Description: None

Sequence

>retro_cpor_1126
ATGGAGGAACTGGATGGGGAACCGGTGGTGACTTTGATTCCAGGTGTGAATTCCAAGAAGCAAATGTGCTTTGACTGGGG
TCCTGGGGAGATACTGGTCTGTGAAACCTCTTCAATCAAAAAGTTTCAGAAACATCTGAGATGGTACCAAGCTGCCCCTT
TATCCATATCATCCGGAAGGACGTAGATGTTTATTCTAAAATTTTGAGAAAACTCTTCAATGAATCACATGGAATCTTTG
TGGGCCTTCAGAGAATTGAAGAAGAATTGAATGGAAAATCCAGAAAAGCTCAATTGGTTCGAGTGAGTAAGAACTACCGA
TCCGTCATAAGAGCGTGTATGGAGGAGATGCACCAGGTTGCACTTGCTGGGAAGGATCAAGCCAGTGGCCACCAATTCAG
CAGCCAGGTCTCCATTTTATCATCGATGGAGCTAATTTGGAACCCGTGTGAGATCCTTTTTATTGAAGTAGCCCCAGCTG
GCCCTCTCCTCCTTCACCTTCTTGACTGGGTCCGGCTCCATGTGTGCGAAGTGGACAGTTTGTTATCAGATGTTCTAGGC
ATTGGAAATCCAAGCAAACATGAGAGCTTCTGGAACTTGGTGACCATCTTGGTGCTGCAGGGCCACCTGGATGAGGCTTG
GCAGATGCTGTCCAGGGAGGCTGATGCCAACCCCACCTCTGGAGACATGTGCCACATCCTGGGGGATCTGATGAGGACAA
TGCCCATTCAAAGCCCTGGCAACACACAGACGCTGACGTAGCTGGAGCTGAAGTGGCAGCACTGGCGCGAGGAGTGCGAG
CAGCACCTGCAGGACAACACATTCGCAGCCAGCCCTGCCCTGGAGTCTCTGTGCAAGATCATGCTGGGGGACGAGGCCAC
CTTGATGGAGCAGAAGGAACTGCTGAATAACTGGTACCATTTCCTTGTGACTCGGCTGCTGTACTCTCACCCCACCGTAA
AGCCTATTGACCTGCACATCTATGCCCAGTCCAGCCTGGACATGTTTCTGGGCGGTGAGAGCAGCCCAGAATCTCTCGAC
AACATCTTGATGGCAGCCTTTGAGTTTGACATCCACCAGGTGATCAAGGAGTGCAGCATCACCCTGAGCAACTGGTGGTT
TGTGGTTCACCTGACAGATCTGCTAGATCACTGCAGGCTCCTCCAGTCCCACAACCTTTATTTTGGTTCCAATATGAGAG
AGTTACTCCTGCTGGAATATGCCTCAGGGCTGTTTGCTCATCACAGCCTGTGGCAGCTGGGGGTGGATTACTTTGACCAC
TGCCCTGAGCTGGGCCATGTTTTCTTGGAGCTGCACATTGAGCAGATCCCTCTCATCCCTGAGTAGAAAGCCCTCAAGGT
GCTTCGGATTTGTGAGCAGTGGCAGATGACGGAACAAGTCCGCAGCATCTGTAAGGTCCTGGCCATGAAAGCCCTCCGTG
ACAATTGTCTGGGCTCTGCCCTCTCTTGGAGCATTCGTGCCAAAGATGCTGCCTTTGCCACACTGGTTTCAGACAGGTTC
CTCAGGGATTACTGTGAGCACGGCTGCTTTTCTGACTTGGATCTCATTGACAACCTGGGGCCAGCCATGATGCTTAGCGA
TCGGTTGACATTCCTAGGGAAGTACCGCGAGTTCCACCGACTGTACGGGGAGAAGTGCTTCAGCGGGGCCTCGGCTCTCC
TCCTGTCCCTGATGACATCTCGGGTTGTTCCGCGCTCTTTCTGGATGACTGTGCTCACAGATGCCCTCCCTCTTCTGGAA
CAGAAACAGGTCATCTTTTCAGCGCTAATGCGATGCTTGGAAGATTCGACCTCAAGGAGGCTGGAATGTGAAGAGCCAGA
TGCCCAGAAACCCCAGGATGATGTCATAGAGACCACCAAGTTGGAGATGCTGAGACTTGCTCTTGCCAGGAATCTTGCTC
GGGCAATTATAAAAGAAGGCTCACTGGAAGGTTCC

Alignment

ORF - retro_cpor_1126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEELDGEPVVTLIPGVNSKKQMCFDWGPGEILVCET-FFNQK--ETSEMVPSCPFIHIIRKDVDVYSKIL
          MEELDGEPVVTLIPGVNSKKQMCFDWGPGEILVCET..FNQK..ETSEMVPSCPFIHIIRKDVDVYSKIL
Retrocopy MEELDGEPVVTLIPGVNSKKQMCFDWGPGEILVCET<LFNQKVSETSEMVPSCPFIHIIRKDVDVYSKIL

Parental  RKLFNESHGIFVGLQRIEEELNGKSRKAQLVRVSKNYRSVIRACMEEMHQVALAGKDGASGHQFSSQVSI
          RKLFNESHGIFVGLQRIEEELNGKSRKAQLVRVSKNYRSVIRACMEEMHQVALAGKD.ASGHQFSSQVSI
Retrocopy RKLFNESHGIFVGLQRIEEELNGKSRKAQLVRVSKNYRSVIRACMEEMHQVALAGKDQASGHQFSSQVSI

Parental  LSAMELIWNLCEILFIEVAPAGPLLLHLLDWVRLHVCEVDSLLADVLGTGNPSKHESFWNLVTILVLQGR
          LS.MELIWN.CEILFIEVAPAGPLLLHLLDWVRLHVCEVDSLL.DVLG.GNPSKHESFWNLVTILVLQG.
Retrocopy LSSMELIWNPCEILFIEVAPAGPLLLHLLDWVRLHVCEVDSLLSDVLGIGNPSKHESFWNLVTILVLQGH

Parental  LDEARQMLSREADANPASGDMCHILGDLMRTMPILSPGNTQTLTELELKWQHWREECERHLQDNTFAASP
          LDEA.QMLSREADANP.SGDMCHILGDLMRTMPI.SPGNTQTLT.LELKWQHWREECE.HLQDNTFAASP
Retrocopy LDEAWQMLSREADANPTSGDMCHILGDLMRTMPIQSPGNTQTLT*LELKWQHWREECEQHLQDNTFAASP

Parental  ALESLCKIMLGDEATLLEQKELLNNWYHFLVTRLLYSHPTVKPIDLHIYAQSSLDMFLGGESSPEPLDNI
          ALESLCKIMLGDEATL.EQKELLNNWYHFLVTRLLYSHPTVKPIDLHIYAQSSLDMFLGGESSPE.LDNI
Retrocopy ALESLCKIMLGDEATLMEQKELLNNWYHFLVTRLLYSHPTVKPIDLHIYAQSSLDMFLGGESSPESLDNI

Parental  LMAAFEFDIHQVIKECSIALSNWWFVAHLTDLLDHCRLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQ
          LMAAFEFDIHQVIKECSI.LSNWWFV.HLTDLLDHCRLLQSHNLYFGSNMRE.LLLEYASGLFAHHSLWQ
Retrocopy LMAAFEFDIHQVIKECSITLSNWWFVVHLTDLLDHCRLLQSHNLYFGSNMRELLLLEYASGLFAHHSLWQ

Parental  LGVDYFDHCPELGRVSLELHIERIPLITEQKALKVLRICEQRQMTEQVRSICKVLAMKALRDSRLGSALS
          LGVDYFDHCPELG.V.LELHIE.IPLI.E.KALKVLRICEQ.QMTEQVRSICKVLAMKALRD..LGSALS
Retrocopy LGVDYFDHCPELGHVFLELHIEQIPLIPE*KALKVLRICEQWQMTEQVRSICKVLAMKALRDNCLGSALS

Parental  WSIRAKDAAFATLVSDRFLRDYCEHGCFSDLDLIDNLGPAMMLSDRLTFLGKYREFHRLYGERCFSGASA
          WSIRAKDAAFATLVSDRFLRDYCEHGCFSDLDLIDNLGPAMMLSDRLTFLGKYREFHRLYGE.CFSGASA
Retrocopy WSIRAKDAAFATLVSDRFLRDYCEHGCFSDLDLIDNLGPAMMLSDRLTFLGKYREFHRLYGEKCFSGASA

Parental  LLLSLMTSRIAPRSFWMTLLTDALPLLEQKQVIFSAEQTYALMRCLEDLTSRKLECEEPDAQKPQDDDIE
          LLLSLMTSR..PRSFWMT.LTDALPLLEQKQVIFSA............L.........P..........E
Retrocopy LLLSLMTSRVVPRSFWMTVLTDALPLLEQKQVIFSALMRCLEDSTSRRLECEEPDAQKPQDDVIETTKLE

Parental  TTKLEMLRLALARNLARAIIKEGSLEGS
          ...L...R..LAR........EGSLEGS
Retrocopy MLRLALAR-NLARAIIK----EGSLEGS

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	0.17 RPM	28.01 RPM
SRP017611_kidney	0.63 RPM	19.68 RPM
SRP017611_liver	0.22 RPM	19.11 RPM
SRP040447_lung	0.03 RPM	28.50 RPM
SRP040447_skeletal_muscle	0.00 RPM	18.03 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1126 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1126 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001185	1 retrocopy	retro_cpor_1126 ,