RetrogeneDB ID: retro_rnor_2342

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:24629938..24630683(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ap2m1
• Ensembl ID: ENSRNOG00000001709
• Aliases: Ap2m1, Ap50, Clapm1, mu2
• Description: AP-2 complex subunit mu [Source:UniProtKB/Swiss-Prot;Acc:P84092]

Sequence

>retro_rnor_2342
TTCATCTATAATCACAAGGGGGAGGTACTTATCTCCTCAGTCTACAGAGATGCCATTGGGAGGAATGCAGTGGATGCCTT
TCGGGTCAGTGTTATTCATGCATGGCAGCAGGTGCACAGCCCTGTCACAAAATCAACCGCACAAGCTTCTTCCCTGTGAA
GCCGTCCAACATCTGGCTGCCAGCAGTCACCAAGCAGAATGTCAATGCTGTCATAGTCTTTGAATTCCTTCACAAGATGT
GTGATGTAATGACTCCTTACTTTGGCAAGATCAGTGAGGAGGACATCAAGAACAATTTTCTGCTCATATATGAGCTGCTG
GACAAGATTCTGGACTTTGGCTACTCACAGAACTCAGAGACAGGTGCACTGAAAACCTTCATCATCCAACAGGGTTTCAA
GAGTCAGCATCAGATAAAAGAAGAGCAGTCCCAGATCACCAGCCAGGTGACCAGGCAGATTGGCTGGTGGTGGGAAGGCA
TCATATATAGCCGGAATGAACTCTTCTAGATGTTCTGGTGAGTGTGAACATGCTTATGTCCCCACAGGGGAAGGTGCCGA
GTTCCCATGTGTCGGGCCAGGTGGCAATGAGTGGCATGCCGGAGTGCAAATTTGGAATTGACAAGATTGTTATAGAAAAG
CAGGGCAAAGGCACAGCTGAAGAAGCAAACAAGAGTGGTAAACAGTCGATCACCACTGATGACTGCCTCTTCCACCGGCT
TGTGCAACTCAGCAGGTTTGACTCT

Alignment

ORF - retro_rnor_2342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.69 %
• Parental protein coverage: 58.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTN-IARTSFFHVKRSNIWLAAVTKQNVN
          FIYNHKGEVLIS.VYRD.IGRNAVDAFRV.VIHA.QQV.SPVT..I.RTSFF.VK.SNIWL.AVTKQNVN
Retrocopy FIYNHKGEVLISSVYRDAIGRNAVDAFRVSVIHAWQQVHSPVTK<INRTSFFPVKPSNIWLPAVTKQNVN

Parental  AAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKSQHQT
          A..VFEFL.KMCDVM..YFGKISEE.IKNNF.LIYELLD.ILDFGY.QNSETGALKTFI.QQG.KSQHQ.
Retrocopy AVIVFEFLHKMCDVMTPYFGKISEEDIKNNFLLIYELLDKILDFGYSQNSETGALKTFIIQQGFKSQHQI

Parental  KEEQSQITSQVTGQIGWRREGIKYRRNELF-LDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECK
          KEEQSQITSQVT.QIGW..EGI.Y.RNELF.LDVL.SVN.LMSPQG.V.S.HVSG.V.M....SGMPECK
Retrocopy KEEQSQITSQVTRQIGWWWEGIIYSRNELF<LDVLVSVNMLMSPQGKVPSSHVSGQVAM----SGMPECK

Parental  FGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDS
          FG..DKIVIEKQGKGTA.E..KSGKQSI..DDC.FH..V.LS.FDS
Retrocopy FGI-DKIVIEKQGKGTAEEANKSGKQSITTDDCLFHRLVQLSRFDS

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	0.14 RPM	563.24 RPM
SRP017611_kidney	0.00 RPM	226.37 RPM
SRP017611_liver	0.00 RPM	63.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2342 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2342 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020106	1 retrocopy	retro_btau_1156,
Canis familiaris	ENSCAFG00000012257	2 retrocopies	retro_cfam_1923, retro_cfam_2028,
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Mus musculus	ENSMUSG00000022841	2 retrocopies	retro_mmus_1873, retro_mmus_1914,
Oryctolagus cuniculus	ENSOCUG00000004556	1 retrocopy	retro_ocun_98,
Otolemur garnettii	ENSOGAG00000012286	1 retrocopy	retro_ogar_1110,
Rattus norvegicus	ENSRNOG00000001709	1 retrocopy	retro_rnor_2342 ,
Tursiops truncatus	ENSTTRG00000008493	1 retrocopy	retro_ttru_522,