RetrogeneDB ID: retro_dord_140

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_3716:246508..247590(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slu7
• Ensembl ID: ENSDORG00000006239
• Aliases: None
• Description: SLU7 splicing factor homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2385598]

Sequence

>retro_dord_140
ATGTCATCGGCAGCTGTGGATACAGTTAATGCCGCGCCTCTGTCCAGGTCCAAAGAACTGAGTTTAGAGGAACCAAAGAA
CATGACTCGAGAGGACTAGAGGAAGGAGCTAGAAGAACAGTGGAAGCTGGGTAATGCTCCTGCAGAAGTGGATGAAGAAG
GAAAAGATATCAATCCACACATCCCTCAGTATATTTCTTCAGTACCATGGTACATCGATCCATGGGAAAGACCCACCTTA
AAGCACCAGAGGCCACAATCTGAGAAACAGAAGCCGTTCAGTTCATCTGGAGAATGGTACAAGAGGGGCGTGAAAGAGAA
TTCCATAACCACTAAGTACCGCAAAGGTGCCTGCGAGAACTGCGGAGCCATGACGCACAAGAAGAAGGACTGCTTCGAGA
GACCCAGGCAAGCCGGCACCAAGTCTACCGGGACTATCATAGCACCAGACGAGCACACCCAGCCTCAGCTCACATTTGAC
TATGCCAGGAAGAGAGATCCCTGGAACGGCTACAATCCAGAACAACACATGAAAATCGTGGAAGAGTACGCCAAAGTCGA
CCTGGCAAAATGAACGCTGAAAGCCCAGAAATTACAAGAAGAATTGTCCTCAGGAAAATCAGCGGAACAAGCTAATTCTC
CAAAGCATCAGTGGGGAGAAGAGGAACCAAATTCTCAGACGGAAAAAATCACAACAGTGAAGATGAGGATGAAGATAAAT
ATGCAGAGGATATTGACCTGCCTGGACAGAATTTTGACTCTAAGAGGCGAATTACAGTCTGGAATCTAAGGATTCGAGAA
GATACTGCAAAATATTTGAGAAATTTAGATCCAAATTCTGCCTACTATGATCCCAAAACTAGAGCGATGAGAGAAAATCC
CTACGCCAATGCAGGGAAGAATCCAGATGAAGTGAGTTATGCAGGCGATAACTTCGTCAGGTACAGAGGTGATACCATTT
CCATGGCTCAGACACAGTTGTCTGCCTGGGAGGCATATGACAAGGGCTCAGAGGTGCGCCTGCAGGAATATCCCACAAAG
CTGGAGCTGTTGTATGAGTCCTTCAAAGAACAGGAGAAAGAA

Alignment

ORF - retro_dord_140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.19 %
• Parental protein coverage: 61.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSAAVDTVNATPLSGSKELSLEEPKKMTREDWRKKKELEEQRKLGNAPAEVDEEGKDINPHIPQYISSV
          MSSAAVDTVNA.PLS.SKELSLEEPK.MTRED.RK..ELEEQ.KLGNAPAEVDEEGKDINPHIPQYISSV
Retrocopy MSSAAVDTVNAAPLSRSKELSLEEPKNMTRED*RK--ELEEQWKLGNAPAEVDEEGKDINPHIPQYISSV

Parental  PWYIDPSKRPTLKHQRPQPEKQKQFSSSAEWYKRGVKENSITTKYRKGACENCGAMTHKKKDCFERPRRV
          PWYIDP..RPTLKHQRPQ.EKQK.FSSS.EWYKRGVKENSITTKYRKGACENCGAMTHKKKDCFERPR..
Retrocopy PWYIDPWERPTLKHQRPQSEKQKPFSSSGEWYKRGVKENSITTKYRKGACENCGAMTHKKKDCFERPRQA

Parental  GAKFTGTNIAPDEHVQPQLTFDYDGKRDRWNGYNPEEHMKIVEEYAKVDLAKRTLKAQKLQEELASGKLV
          G.K.TGT.IAPDEH.QPQLTFDY..KRD.WNGYNPE.HMKIVEEYAKVDLAK.TLKAQKLQEEL.SGK..
Retrocopy GTKSTGTIIAPDEHTQPQLTFDYARKRDPWNGYNPEQHMKIVEEYAKVDLAK*TLKAQKLQEELSSGKSA

Parental  EQANSPKHQWGEEEPNSQTE-KDHNSEDEDEDKYADDIDMPGQNFDSKRRITVRNLRIREDIAKYLRNLD
          EQANSPKHQWGEEEPNSQTE.K.HNSEDEDEDKYA.DID.PGQNFDSKRRITV.NLRIRED.AKYLRNLD
Retrocopy EQANSPKHQWGEEEPNSQTE<KNHNSEDEDEDKYAEDIDLPGQNFDSKRRITVWNLRIREDTAKYLRNLD

Parental  PNSAYYDPKTRAMRENPYANAGKNPDEVSYAGDNFVRYTGDTISMAQTQLFAWEAYDKGSEVHLQADPTK
          PNSAYYDPKTRAMRENPYANAGKNPDEVSYAGDNFVRY.GDTISMAQTQL.AWEAYDKGSEV.LQ..PTK
Retrocopy PNSAYYDPKTRAMRENPYANAGKNPDEVSYAGDNFVRYRGDTISMAQTQLSAWEAYDKGSEVRLQEYPTK

Parental  LELLYKSFKVKKED
          LELLY.SFK.....
Retrocopy LELLYESFKEQEKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_140 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004484	1 retrocopy	retro_cpor_883,
Dipodomys ordii	ENSDORG00000006239	3 retrocopies	retro_dord_125, retro_dord_140 , retro_dord_563,
Ficedula albicollis	ENSFALG00000013473	1 retrocopy	retro_falb_12,
Myotis lucifugus	ENSMLUG00000003091	2 retrocopies	retro_mluc_2250, retro_mluc_2251,
Oryctolagus cuniculus	ENSOCUG00000011743	1 retrocopy	retro_ocun_818,
Otolemur garnettii	ENSOGAG00000012301	1 retrocopy	retro_ogar_1519,
Sorex araneus	ENSSARG00000012209	2 retrocopies	retro_sara_409, retro_sara_731,