RetrogeneDB ID: retro_rnor_2032

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:3174793..3175977(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000050173
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mat2a
• Ensembl ID: ENSRNOG00000013520
• Aliases: Mat2a, Sams2
• Description: S-adenosylmethionine synthase isoform type-2 [Source:RefSeq peptide;Acc:NP_599178]

Sequence

>retro_rnor_2032
ATGAACCGGCAGCTCAACGGCTTCCATGAGGCATTCATTGAAGAGGGGACATTCCTTTTCACTTCAGAGTCTGTAGGGGA
AGGTCACCCAGATAAGATTTGTGACCAAATCAGTGATGCTGTCCTTGATGCACACCTTCAGCAGGACCCTGATCCTAAAG
TGGCTTGTGAAACTGTTGCTAAAACTGGAATGATCCTTCTTGCTGGGGAAATTACATCTAGAGCTGCCATTGATTACCAG
AAAGTGGTTCGTGAAGCCATAAAGCACATTAGCTATGATGATTCTTCCAAAGGGTTTGACTACAAGACTTGTAATGTGTT
GGTTGCCTTGGAACAACAGTCACCAGATATCGCCCAAGGTGTTCATCTTGACCGAAATGAGGAAGACCATGGTGCAGGAG
ATCAGGGTTTGATGTTTGGTTATGCCACTGATGAAACTGAAGAGTGTATGCCTTTAACTATTGTCTTAGCACACAAGCTA
AATGCTAAACTGGCTGAGCTACGCCGCAATGGCACATTGCCTTGGTTACGCCCAGATTCTAAAACTCAAGTGACTGTGCA
GTATATGCAAGATCGAGGTGCTGTGATTCCCATCAGAGTCCACACAATTGTCATATCTGTTCAGCATGATGAAGAAGTTT
GTCTTGATGAGATGAGGGATGCTCTGAAGGAGAAAGTGATCAAAGCTGTTGTACATGCAAAGTACCTTGATGAGGATACA
ATTTACCACATACAGCCAAGTGGCAGATTCGTTATTGGTGGGCCTCAGGGTGATGCCGGTTTGACTGGCCGAAAAATCAT
TGTGGATACTTATGGCGGTTGGGGAGCTCATGGAGGAGGGGCCTTTTCAGGAAAGGATTATACCAAAGTGGACCGTTCAG
CTGCTTATGCTGCTCGTTGGGTGGCAAAAACCCTTGTTAAAGGAGGTCTGTGCAGGAGGGTTCTGTTCAGGTCTCTTATG
CTATTGGAGTTTCTCATCCATTGTCGATCTCCATTTTCCATTATGGTACTTCTCAGAAGAGTGCGAGAGAGCTATTAGAA
ATTGTGAAGAATAATTTTGATCTTCGCCCTGGGGTCATTGTCAGGGATCTGGATCTGAAGAAGCCAATTTATCAGAGGAC
TGCAGCTTATGGCCACTTTGGTAGGGACAGCTTCCCCTGGGAAGTGCCCAAAAAGCTTAAATAT

Alignment

ORF - retro_rnor_2032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGE
          MN.QLNGFHEAFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPD.KVACETVAKTGMILLAGE
Retrocopy MNRQLNGFHEAFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDPKVACETVAKTGMILLAGE

Parental  ITSRAAIDYQKVVREAIKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFG
          ITSRAAIDYQKVVREAIKHI.YDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEED.GAGDQGLMFG
Retrocopy ITSRAAIDYQKVVREAIKHISYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDHGAGDQGLMFG

Parental  YATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVIPIRVHTIVISVQHD
          YATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVIPIRVHTIVISVQHD
Retrocopy YATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVIPIRVHTIVISVQHD

Parental  EEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGG
          EEVCLDEMRDALKEKVIKAVV.AKYLDEDTIYH.QPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGG
Retrocopy EEVCLDEMRDALKEKVIKAVVHAKYLDEDTIYHIQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGG

Parental  AFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVL-VQVSYAIGVSHPLSISIFHYGTSQKSERELLEIV
          AFSGKDYTKVDRSAAYAARWVAK.LVKGGLCRRVL.VQVSYAIGVSHPLSISIFHYGTSQKS.RELLEIV
Retrocopy AFSGKDYTKVDRSAAYAARWVAKTLVKGGLCRRVL<VQVSYAIGVSHPLSISIFHYGTSQKSARELLEIV

Parental  KNNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY
          KNNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY
Retrocopy KNNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY

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	0.07 RPM	68.16 RPM
SRP017611_kidney	0.49 RPM	280.87 RPM
SRP017611_liver	0.00 RPM	14.25 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2032 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2032 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013959	1 retrocopy	retro_chof_30,
Echinops telfairi	ENSETEG00000007634	2 retrocopies	retro_etel_1308, retro_etel_1532,
Echinops telfairi	ENSETEG00000015680	4 retrocopies	retro_etel_1669, retro_etel_1813, retro_etel_597, retro_etel_977,
Ornithorhynchus anatinus	ENSOANG00000003060	1 retrocopy	retro_oana_84,
Otolemur garnettii	ENSOGAG00000026925	1 retrocopy	retro_ogar_1580,
Rattus norvegicus	ENSRNOG00000013520	2 retrocopies	retro_rnor_2032 , retro_rnor_955,