RetrogeneDB ID: retro_rnor_791

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:31671031..31672309(+)
• Located in intron of: ENSRNOG00000001575

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snx1
• Ensembl ID: ENSRNOG00000017029
• Aliases: None
• Description: Sorting nexin-1 [Source:UniProtKB/Swiss-Prot;Acc:Q99N27]

Sequence

>retro_rnor_791
CTATCCCTGGATAGCACACAGAATAACCAGAAGACAATGCCAGGCAAAACACTTATTCCTCATCCTACGCAAGAAGCCAC
AAATTCTCCTAAGCCACAGCCAAGCTATGAAGAGCTGGAGGAAGAACAGGAGGATCAGTTTGATTTGACAGTTGGTATCA
CTGATCCTGAGAAGATCGGGGACGGTATGAATGCCTATGTAGCCTACAAAGTCACCACACAGACAAGCTTACCGATGTTC
AGAAGTAGGCAGTTTGCAGTGAAAAGAAGATTCAGTGACTTTCTGGGTCTTTATGAGAAGCTCTCAGAGAAGCACTCCCA
GAATGGTTTCATTGTCCCTCCTCCACCTGAGAAGAGCCTAATAGGAATGACAAAGGTGAAGGTTGGGAAGGAAGATTCTT
CTTCTGCAGAGTTTCTTGAGAAACGGAGGGCTGCTTTGGAAAGGTACCTTCAAAGAATTGTGAATCATCCTACCATGTTA
CAGGACCCAGATGTCAGGGAGTTTTTAGAAAAAGAAGAGCTGCCTCGAGCTGTAGGTACGCGGGCTCTAAGTGGTGCTGG
TCTCCTTAAGATGTTCAACAAAGCTACAGATGCAGTCAGCAAAATGACCATCAAGATGAATGAATCAGACATTTGGTTCG
AGGAGAAGCTCCAGGAGGTGGAGTGTGAGGAACAGCGCCTACGGAAGCTGCACGCTGTGGTGGAGACTCTAGTCAACCAT
AGGAAAGAACTAGCACTGAATACAGCCCTGTTTGCCAAGAGTCTAGCCATGCTTGGCAGCTCCGAGGACAACACAGCACT
GTCTCGAGCACTCTCCCAACTGGCTGAGGTGGAAGAAAAGATTGAGCAGCTCCACCAGGAACAGGCCAACAATGACTTCT
TCCTCCTGGCTGAACTCCTGAGTGACTATATCCGCCTCCTGGCCATTGTCCGAGCCGCCTTCGACCAGCGCATGAAGACA
TGGCAGCGCTGGCAGGATGCTCAAGCCACACTGCAGAAGAAGCGGGAGTCTGAGGCTCGGCTGCTGTGGGCCAACAAGCC
TGACAAACTGCAGCAGGCTAAGGATGAGATTACAGAGTGGGAATCTCGGGTGACTCAGTATGAAAGGGACTTTGAAAGGA
TTTCAACAGTTGTCCGAAAGGAGGTGACACGATTTGAGAAAGAGAAATCCAAGGACTTCAAAAACCACGTGATCAAGTAC
CTGGAGACACTCCTGCATTCCCAGCAGCAGCTGGCAAAATACTGGGAAGCCTTCCTTCCTGAGGCCAGGGCCATCTCC

Alignment

ORF - retro_rnor_791 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.53 %
• Parental protein coverage: 81.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSLDSTQNNQKTMPGKTLIPHPTQEATNSPKPQPSYEELEEEEQEDQFDLTVGITDPEKIGDGMNAYVAY
          LSLDSTQNNQKTMPGKTLIPHPTQEATNSPKPQPSYEELEEE.QEDQFDLTVGITDPEKIGDGMNAYVAY
Retrocopy LSLDSTQNNQKTMPGKTLIPHPTQEATNSPKPQPSYEELEEE-QEDQFDLTVGITDPEKIGDGMNAYVAY

Parental  KVTTQTSLPMFRSRQFAVKRRFSDFLGLYEKLSEKHSQNGFIVPPPPEKSLIGMTKVKVGKEDSSSAEFL
          KVTTQTSLPMFRSRQFAVKRRFSDFLGLYEKLSEKHSQNGFIVPPPPEKSLIGMTKVKVGKEDSSSAEFL
Retrocopy KVTTQTSLPMFRSRQFAVKRRFSDFLGLYEKLSEKHSQNGFIVPPPPEKSLIGMTKVKVGKEDSSSAEFL

Parental  EKRRAALERYLQRIVNHPTMLQDPDVREFLEKEELPRAVGTQALSGAGLLKMFNKATDAVSKMTIKMNES
          EKRRAALERYLQRIVNHPTMLQDPDVREFLEKEELPRAVGT.ALSGAGLLKMFNKATDAVSKMTIKMNES
Retrocopy EKRRAALERYLQRIVNHPTMLQDPDVREFLEKEELPRAVGTRALSGAGLLKMFNKATDAVSKMTIKMNES

Parental  DIWFEEKLQEVECEEQRLRKLHAVVETLVNHRKELALNTALFAKSLAMLGSSEDNTALSRALSQLAEVEE
          DIWFEEKLQEVECEEQRLRKLHAVVETLVNHRKELALNTALFAKSLAMLGSSEDNTALSRALSQLAEVEE
Retrocopy DIWFEEKLQEVECEEQRLRKLHAVVETLVNHRKELALNTALFAKSLAMLGSSEDNTALSRALSQLAEVEE

Parental  KIEQLHQEQANNDFFLLAELLSDYIRLLAIVRAAFDQRMKTWQRWQDAQATLQKKRESEARLLWANKPDK
          KIEQLHQEQANNDFFLLAELLSDYIRLLAIVRAAFDQRMKTWQRWQDAQATLQKKRESEARLLWANKPDK
Retrocopy KIEQLHQEQANNDFFLLAELLSDYIRLLAIVRAAFDQRMKTWQRWQDAQATLQKKRESEARLLWANKPDK

Parental  LQQAKDEITEWESRVTQYERDFERISTVVRKEVTRFEKEKSKDFKNHVIKYLETLLHSQQQLAKYWEAFL
          LQQAKDEITEWESRVTQYERDFERISTVVRKEVTRFEKEKSKDFKNHVIKYLETLLHSQQQLAKYWEAFL
Retrocopy LQQAKDEITEWESRVTQYERDFERISTVVRKEVTRFEKEKSKDFKNHVIKYLETLLHSQQQLAKYWEAFL

Parental  PEARAIS
          PEARAIS
Retrocopy PEARAIS

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	0.43 RPM	20.13 RPM
SRP017611_kidney	0.28 RPM	31.54 RPM
SRP017611_liver	0.13 RPM	7.06 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_rnor_791 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB700836	31671645	31671929	96.9	273	9	264
DV717497	31671648	31671814	100	163	0	163
DV717499	31671648	31671774	100	122	0	122

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_791 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_791 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
Choloepus hoffmanni	ENSCHOG00000000707	2 retrocopies	retro_chof_2390, retro_chof_265,
Rattus norvegicus	ENSRNOG00000017029	1 retrocopy	retro_rnor_791 ,