RetrogeneDB ID: retro_rnor_600

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:121131789..121133310(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mgat4a
• Ensembl ID: ENSRNOG00000018276
• Aliases: None
• Description: alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A isoform 1 [Source:RefSeq peptide;Acc:NP_001153627]

Sequence

>retro_rnor_600
AGAGAAAAATTAATTGCTTACCAACGAGAATTCCTCGCTTGAAAAGAACGTCTTCGAGTGGCCGAACATAGGATATCTCA
GCGCTCCTCTGAGCTAAACACCATTGTCCAACAGTTCCGCCGAGCTGGAGCGGAGACTAATGGAAGTAAGGCTGGTCTGA
GTACGTTCTAAGATAATACCATAAAGCTTCTAAAAGAGTTGACAAGCAAAAAATCACTTCAAGTGCCAAGTATTTATTAT
CATTTGCCTCATCTATTGCAAAATGAAAGAAGCCTTCAGCCCGCCGTACAGATTGGCAGTGGAAGAACGGGAGTTTCAAT
AGTCATGGGGATTCCTACTGTAAAGAGAGAAGTTAAATCTTACCTCATAGAGACCCTTCACTCCCTTATTGATAATCTGT
ATCCTGAAGAGAAGCTGGACTGTGTTATAGTTGTCTTCATAGGAGAGACAGATCTTGATTATGTTCACAGCGTTGTTGCC
AACCTGGAGAAAGAATTTTCTAGAGAAATTAGTTCCGGCTTGCTAGAAGTAATCTCTCCTCCTGAAAGCTATTACCCCGA
CTTAACAAACCTGAAGGAGACGTCCGGAGACTCCAAGGAAAGAGTAAGATGGAGAAGGAGAACGAAGCAAAACCTGGACT
ATTGTTTTCTGATGATGTATGCTCAGGAGAAGGGCATTTACTACATTCAGCTTGAAGATGATATTATTGTCAAGCAAAAC
TATTTTAATACCATAAAAAATTTTGCACTTCAACTTTCTTCTGAAGAATGGATGATTCTAGAGTTTTCCCAGCTGGGCTT
CATTGGGAAGATGTTCCAGGCGCCGGACCTAGCTCTGGTTGTGGAGTTCATTCTCATGTTCTATAAGGAGAAGCCCATTG
ACTGGCTCTTGGACCACATTCTCTGGGTGAAGATCTGCAACCCCGAAAAAGATGCCAAACACTGTGACAGACAGAAGGCA
AACCTACGAATCCGCTTCCGACCCTCCCTCTTCCAGCACGTGGGTCTACACTCATCTCTGTCGGGGAAAATTCAGAAACT
TACGGATAAAGATTACATGAAACCATTGCTTCTCAAGATCCACGTGAACCTGCCTGCAGAGGTCTCCACTTCCCTGAAGG
TGTACCAAGGGCACACACTGGAGAAGACCTACATGGGGGAAGACTTCTTTTGGGCCATCACCCCCACAGCTGGAGACTAC
ATCTTGTTTAAATTCGACAAACCGGTCAATGTGGAGAGTTATTTGTTCCACAGCGGCAATCAAGAGCACCCAGGGGACAT
CCTGCTGAACACGACCGTGGAGGTTCTGCCTCTTAAGAGCGACAGTTTGGAGATCAGCAAAGAAATCAAAGACAAACGAT
TAGAAGATGGCTATTTCAGAATAGGGAAATTTGAGTACGGAGTTGCAGAGGGAATTGTGGATCCTGGACTGAACCCTATC
TCAGCCTTTCGACTGTCGGTTATTCAGAACTCTGCTGTCTGGGCCATTCTCAATGAGATTCATATTAAGAAAGTCACCAG
T

Alignment

ORF - retro_rnor_600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.22 %
• Parental protein coverage: 94.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEKLIAYQREFLALKERLRVAEHRISQRSSELNTIVQQFRRAGAETNGSKAGLSTFSDNTIKLLKELTSK
          .EKLIAYQREFLA.KERLRVAEHRISQRSSELNTIVQQFRRAGAETNGSKAGLSTF.DNTIKLLKELTSK
Retrocopy REKLIAYQREFLA*KERLRVAEHRISQRSSELNTIVQQFRRAGAETNGSKAGLSTF*DNTIKLLKELTSK

Parental  KSLQVPSIYYHLPHLLQNERSLQPAVQIGSGRTGVSIVMGIPTVKREVKSYLIETLHSLIDNLYPEEKLD
          KSLQVPSIYYHLPHLLQNERSLQPAVQIGSGRTGVSIVMGIPTVKREVKSYLIETLHSLIDNLYPEEKLD
Retrocopy KSLQVPSIYYHLPHLLQNERSLQPAVQIGSGRTGVSIVMGIPTVKREVKSYLIETLHSLIDNLYPEEKLD

Parental  CVIVVFIGETDLDYVHSVVANLEKEFSREISSGLLEVISPPESYYPDLTNLKETFGDSKERVRW--RTKQ
          CVIVVFIGETDLDYVHSVVANLEKEFSREISSGLLEVISPPESYYPDLTNLKET.GDSKERVRW..RTKQ
Retrocopy CVIVVFIGETDLDYVHSVVANLEKEFSREISSGLLEVISPPESYYPDLTNLKETSGDSKERVRWRRRTKQ

Parental  NLDYCFLMMYAQEKGIYYIQLEDDIIVKQNYFNTIKNFALQLSSEEWMILEFSQLGFIGKMFQAPDLALV
          NLDYCFLMMYAQEKGIYYIQLEDDIIVKQNYFNTIKNFALQLSSEEWMILEFSQLGFIGKMFQAPDLALV
Retrocopy NLDYCFLMMYAQEKGIYYIQLEDDIIVKQNYFNTIKNFALQLSSEEWMILEFSQLGFIGKMFQAPDLALV

Parental  VEFILMFYKEKPIDWLLDHILWVKVCNPEKDAKHCDRQKANLRIRFRPSLFQHVGLHSSLSGKIQKLTDK
          VEFILMFYKEKPIDWLLDHILWVK.CNPEKDAKHCDRQKANLRIRFRPSLFQHVGLHSSLSGKIQKLTDK
Retrocopy VEFILMFYKEKPIDWLLDHILWVKICNPEKDAKHCDRQKANLRIRFRPSLFQHVGLHSSLSGKIQKLTDK

Parental  DYMKPLLLKIHVNPPAEVSTSLKVYQGHTLEKTYMGEDFFWAITPTAGDYILFKFDKPVNVESYLFHSGN
          DYMKPLLLKIHVN.PAEVSTSLKVYQGHTLEKTYMGEDFFWAITPTAGDYILFKFDKPVNVESYLFHSGN
Retrocopy DYMKPLLLKIHVNLPAEVSTSLKVYQGHTLEKTYMGEDFFWAITPTAGDYILFKFDKPVNVESYLFHSGN

Parental  QEHPGDILLNTTVEVLPLKSDSLEISKETKDKRLEDGYFRIGKFEYGVAEGIVDPGLNPISAFRLSVIQN
          QEHPGDILLNTTVEVLPLKSDSLEISKE.KDKRLEDGYFRIGKFEYGVAEGIVDPGLNPISAFRLSVIQN
Retrocopy QEHPGDILLNTTVEVLPLKSDSLEISKEIKDKRLEDGYFRIGKFEYGVAEGIVDPGLNPISAFRLSVIQN

Parental  SAVWAILNEIHIKKVTS
          SAVWAILNEIHIKKVTS
Retrocopy SAVWAILNEIHIKKVTS

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	20.78 RPM
SRP017611_kidney	0.00 RPM	41.87 RPM
SRP017611_liver	0.00 RPM	0.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_600 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_600 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000011487	1 retrocopy	retro_ogar_1805,
Rattus norvegicus	ENSRNOG00000018276	2 retrocopies	retro_rnor_600 , retro_rnor_601,