RetrogeneDB ID: retro_rnor_939

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:98347244..98348945(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Uba2
• Ensembl ID: ENSRNOG00000021113
• Aliases: Uba2, Sae2, Uble1b
• Description: SUMO-activating enzyme subunit 2 [Source:RefSeq peptide;Acc:NP_001094049]

Sequence

>retro_rnor_939
GCTCAGGTTGCCAAAGAAAGTGTGCTTCAGTTCCACCCCCAAGCGAACATTGAGGCCCACCATGACAGCATCATGAACCC
AGACTATAATGTGGAGTTTTTTCGACAGTTTATATTGGTTATGAACGCATTAGATAACAGAGCTGCACGAAACCATGTGA
ATAGGATGTGTCTGGCAGCTGACATGCCTCTCATTGAGAGTGGGACTGCTGGGTATCTTGGACAGGTGACCATGATCAAG
AAGGGTGTGACTGAGTGTTACGAATGTCATCCTAAGCCGACCCAGAGAACGTTCCCTGGCTGTACGATTCGGAACACACC
TTCAGAACCTATCCATTGCATCGTATGGGCCAAGTATTTGTTCAACCAGCTGTTTGGAGAGGAAGATGCTGATCAAGAAG
TGTCTCCTGACAGAGCTGACCCTGAAGCTGCTTGGGAACCAACAGAGGCTGAAGCCAGAGCCCGAGCATCCAATGAAGAT
GGAGACATTAAGCGGATTTCCACTAAGGAATGGGCTAAGTCAACTGGATACGATCCAGTTAAACTTTTTACCAAGCTTTT
TAAAGATGATATTAGGTATCTGCTGACAATGGACAAACTCTGGCGCAAGAGGAAACCTCCAGTTCCACTGGACTGGGCTG
AAGTGCAGAGTCAAGGAGAAGAAGCCAATGCTGATCAACAAAGTGAGCCCCAGTTGGGTTTGAAAGACCAGCAGGTTCTG
GATGTAAAGAGCTACACAAGTCTGTTTTCAAAGAGCATCGAGACCCTGAGAGTCCGTTTAGCCGAGAAGGGAGATGGAGC
TGAGCTCATCTGGGATAAGGACGACCCACCTGCAATGGATTTTGTCACGTCTGCTGCAAACCTCAGGATGCACATTTTCA
GCATGAACATGAAGAGCAGGTTTGATATAAAATCAATGGCGGGGAACATCATCCCTGCTATAGCCACCACTAATGCAGTG
ATCGCCGGCTTGATAGTGTTGGAAGGATTAAAGATTTTATCTGGAAAAATAGACCAGTGTAGAACTATATTTTTGAATAA
GCAGCCAAACCCGAGAAAGAAGCTCTTGGTGCCCTGTGCACTAGATCCTCCCAACACCAACTGTTACGTTTGTGCCAGCA
AGCCAGAGGTGACCGTGCGGCTGAATGTCCACAAAGTGACTGTCCTCACCTTACAGGATAAGATAGTGAAAGAAAAGTTT
GCTATGGTGGCACCAGATGTCCAAATTGAAGATGGGAAAGGCACAATCCTGATATCTTCAGAAGAGGGAGAGACAGAAGC
TAATAACCCCAAGAAGTTGTCTGATTTTGGAATTAGAAATGGCAGCCGGCTTCAAGCAGACGACTTCCTGTAGGACTACA
CTTTGCTGATCAACATTCTTCATAGCGAGGATCTAGGAAAGGATGTTGAATTTGAGGTAGTTGGTGACACCCCTGAAAAA
GTGGGTCCAAAACAAGCTGAAGACGCTGCCAAAAGCATTGCCAACGGCAGCGATGATGGCGCCCAGCCTTCCACCTCCAC
AGCACAAGAACAAGATGATGTGCTCATAGTTGATTCAGATGAAGAAGGCCCTTCAAATAGCGCCGACGGTAGCAGGGACG
ATAGGACCCGCAAGCGGAAACTGGAAGAGAATGAGGGTGCCAGTACCAAGAAGTCCCGCTTGGAGCAGGTGGAAGATCAG
GATGACGTCATAGCATTAGAC

Alignment

ORF - retro_rnor_939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQVAKESVLQFHPQANIEAHHDSIMNPDYNVEFFRQFILVMNALDNRAARNHVNRMCLAADVPLIESGTA
          .QVAKESVLQFHPQANIEAHHDSIMNPDYNVEFFRQFILVMNALDNRAARNHVNRMCLAAD.PLIESGTA
Retrocopy AQVAKESVLQFHPQANIEAHHDSIMNPDYNVEFFRQFILVMNALDNRAARNHVNRMCLAADMPLIESGTA

Parental  GYLGQVTTIKKGVTECYECHPKPTQRTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRAD
          GYLGQVT.IKKGVTECYECHPKPTQRTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRAD
Retrocopy GYLGQVTMIKKGVTECYECHPKPTQRTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRAD

Parental  PEAAWEPTEAEARARASNEDGDIKRISTKEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPL
          PEAAWEPTEAEARARASNEDGDIKRISTKEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPL
Retrocopy PEAAWEPTEAEARARASNEDGDIKRISTKEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPL

Parental  DWAEVQSQGEEANADQQSEPQLGLKDQQVLDVKSYASLFSKSIETLRVRLAEKGDGAELIWDKDDPPAMD
          DWAEVQSQGEEANADQQSEPQLGLKDQQVLDVKSY.SLFSKSIETLRVRLAEKGDGAELIWDKDDPPAMD
Retrocopy DWAEVQSQGEEANADQQSEPQLGLKDQQVLDVKSYTSLFSKSIETLRVRLAEKGDGAELIWDKDDPPAMD

Parental  FVTSAANLRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNKQPN
          FVTSAANLRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNKQPN
Retrocopy FVTSAANLRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNKQPN

Parental  PRKKLLVPCALDPPNTNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDVQIEDGKGTILISS
          PRKKLLVPCALDPPNTNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDVQIEDGKGTILISS
Retrocopy PRKKLLVPCALDPPNTNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDVQIEDGKGTILISS

Parental  EEGETEANNPKKLSDFGIRNGSRLQADDFLQDYTLLINILHSEDLGKDVEFEVVGDTPEKVGPKQAEDAA
          EEGETEANNPKKLSDFGIRNGSRLQADDFL.DYTLLINILHSEDLGKDVEFEVVGDTPEKVGPKQAEDAA
Retrocopy EEGETEANNPKKLSDFGIRNGSRLQADDFL*DYTLLINILHSEDLGKDVEFEVVGDTPEKVGPKQAEDAA

Parental  KSIANGSDDGAQPSTSTEQAQEQDDVLIVDSDEEGPSNSADGSRDDRTRKRKLEENEGASTKKSRLEQVE
          KSIANGSDDGAQPSTST..AQEQDDVLIVDSDEEGPSNSADGSRDDRTRKRKLEENEGASTKKSRLEQVE
Retrocopy KSIANGSDDGAQPSTST--AQEQDDVLIVDSDEEGPSNSADGSRDDRTRKRKLEENEGASTKKSRLEQVE

Parental  DQDDVIALD
          DQDDVIALD
Retrocopy DQDDVIALD

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	6.69 RPM	17.26 RPM
SRP017611_kidney	4.05 RPM	13.19 RPM
SRP017611_liver	2.02 RPM	6.32 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_rnor_939 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG663354	98348026	98348467	100	441	0	441
CD372081	98347610	98348327	99.5	710	3	705
H34481	98347660	98347919	99.7	254	1	253

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_939 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011975	3 retrocopies	retro_chof_1034, retro_chof_548, retro_chof_848,
Myotis lucifugus	ENSMLUG00000003047	1 retrocopy	retro_mluc_286,
Monodelphis domestica	ENSMODG00000011934	1 retrocopy	retro_mdom_1509,
Pongo abelii	ENSPPYG00000009837	1 retrocopy	retro_pabe_304,
Rattus norvegicus	ENSRNOG00000021113	1 retrocopy	retro_rnor_939 ,
Sus scrofa	ENSSSCG00000002876	1 retrocopy	retro_sscr_941,