RetrogeneDB ID: retro_dord_125

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_3716:289882..291622(+)
• 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_125
ATGTCATTGGCAGCTGTGGATACAGTTAATGCCACACCCCTGTCGGGGTCCAAAGAACTGAGTTTAGAGGAACCAAAGAA
GATGACCCGAGAGGACTGGAGGAAGAAGAAGGAGCTAGAAGAACAGCGGAAGCTGGGTAATGCTCCTGCAGAAGTGGATG
AAGAAGGAAAAGATATCAATCCACACATCCCTCAGTATATTTCTTCAGTACCATGGTACATCGATCCATGGAAAAGACCC
ACCTTAAAGCACCAGAGGCCACAATCTGAGAAACAGAAGCCGTTCAGTTCATCTGGAGAATGGTACAAGAGGGGCGTAAA
AGAGAATTCCATAACCACTAAGTACCGCAAAGGTGCCTGCGAGAACTGCGGAGCCATGACGCACAAGAAGAAGGACTGCT
TTGAGAGACCCAGACGAATTGGGGCCAAGTTTACTGGGACTAACATGGCGCCAGATGAGCACGTCCAGCCTCAGCTCACA
TTTGACTACGACGGGAAGAGAGATCGCTGGAATGGCTACAATCCAGAGGAACACATGAAAATCGTGGAAGAGTACGCCAA
AGTCGACCTGGCAAAACGAACGCTGAAAGCCCAGAAATTACAAGAAGAATTGGCCTCAGGAAAATTAGTGGAACAGGCTA
ATTCTCCAAAACAGTGGGGAGAAGAGGAACCAAATTCTCAGATGGAAAAAGATCACAACAGTGAAGATGAGGATGAAGAT
AAATATGCAGAGGATATTGACCTGCCTGGACAGAATTTTGACTCTAAGAGGCGAATTACAGTCCGGAACCTAAGGATTCG
AGAAGATATTGCAAAATATTTGAGAAATTTAGATCCAAATTCTGCCTACTATGATCCCAAAACTAGAGCGATGAGAGAAA
ATCCCTACGCCAATGCAGGGAAGAATCCAGATGAAGTGAGTTATGCAGGCGATAACTTCGTCAGATACACAGGAGATACC
ATTTCCATGGCTCAGACACAGTTGTTTGCCTGGGAGGCATTTGACAAGGGCTCGGAGGTGCACTTGCAGGCAGATCCCAC
GAAGCTGGAGCTGTTGTATAAATCCTTCAAAGTCAAGAAGGAAGACTTCAAAGTACAGCAGAAAGAAAGCATCCTGGAAA
AGTATGGTGGCCAAGAGCATCTGGATGCTCCTCCTGCTGGGTTGCTCTTAGCCCAGACGGAAGACTACGTGGAGTACTCA
CGGCATGGGGCCGTCATCAAGGGGCAGGAGAGGGCCGTGGCCTGCTCCAAGTATGAAGAGGACGTGAAGATCCACAACCA
CACGCACATCTGGGGATCTTACTGGAAAGAAGGCCGATGGGGATACAAATGCTGTCACTCGTTCTTCAAGTATTCCTACT
GCACTGGAGAAGCTGGGAAGGAGACTGCTAACGCCAAGGAGTGTGTGATAAGTGATGAGACTGGCAAAGAGTCGGTGAAG
AAACCACAGACGCTCGTGGAGATGCACCAAGAAAAACTAAAGGAAGAGAAGAAAAAGAAGCACCGGAAGAGCAGCTCTGA
AAGCGATGACAAAGAGAAGAAACAGGAGAAACTGAAGAAGGCACTGAATGCCGAGAAGGCCCGCCTGCTCCACGTCAAGG
AGATCTTACAAATTGACAAGAGAAAGCGGCCATACAACAGTGTATATGAAACTCGAGAGCCCACGGAGGAGGAAATGGAG
ACCTACAGAATGAAACGTCAGAGGCCAGATGACCCCATGGCCTGTTTCCTGGGCCAGCAG

Alignment

ORF - retro_dord_125 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSAAVDTVNATPLSGSKELSLEEPKKMTREDWRKKKELEEQRKLGNAPAEVDEEGKDINPHIPQYISSV
          MS.AAVDTVNATPLSGSKELSLEEPKKMTREDWRKKKELEEQRKLGNAPAEVDEEGKDINPHIPQYISSV
Retrocopy MSLAAVDTVNATPLSGSKELSLEEPKKMTREDWRKKKELEEQRKLGNAPAEVDEEGKDINPHIPQYISSV

Parental  PWYIDPSKRPTLKHQRPQPEKQKQFSSSAEWYKRGVKENSITTKYRKGACENCGAMTHKKKDCFERPRRV
          PWYIDP.KRPTLKHQRPQ.EKQK.FSSS.EWYKRGVKENSITTKYRKGACENCGAMTHKKKDCFERPRR.
Retrocopy PWYIDPWKRPTLKHQRPQSEKQKPFSSSGEWYKRGVKENSITTKYRKGACENCGAMTHKKKDCFERPRRI

Parental  GAKFTGTNIAPDEHVQPQLTFDYDGKRDRWNGYNPEEHMKIVEEYAKVDLAKRTLKAQKLQEELASGKLV
          GAKFTGTN.APDEHVQPQLTFDYDGKRDRWNGYNPEEHMKIVEEYAKVDLAKRTLKAQKLQEELASGKLV
Retrocopy GAKFTGTNMAPDEHVQPQLTFDYDGKRDRWNGYNPEEHMKIVEEYAKVDLAKRTLKAQKLQEELASGKLV

Parental  EQANSPKHQWGEEEPNSQTEKDHNSEDEDEDKYADDIDMPGQNFDSKRRITVRNLRIREDIAKYLRNLDP
          EQANSPK.QWGEEEPNSQ.EKDHNSEDEDEDKYA.DID.PGQNFDSKRRITVRNLRIREDIAKYLRNLDP
Retrocopy EQANSPK-QWGEEEPNSQMEKDHNSEDEDEDKYAEDIDLPGQNFDSKRRITVRNLRIREDIAKYLRNLDP

Parental  NSAYYDPKTRAMRENPYANAGKNPDEVSYAGDNFVRYTGDTISMAQTQLFAWEAYDKGSEVHLQADPTKL
          NSAYYDPKTRAMRENPYANAGKNPDEVSYAGDNFVRYTGDTISMAQTQLFAWEA.DKGSEVHLQADPTKL
Retrocopy NSAYYDPKTRAMRENPYANAGKNPDEVSYAGDNFVRYTGDTISMAQTQLFAWEAFDKGSEVHLQADPTKL

Parental  ELLYKSFKVKKEDFKEQQKESILEKYGGQEHLDAPPAELLLAQTEDYVEYSRHGAVIKGQERAVACSKYE
          ELLYK...............SILEKYGGQEHLDAPPA.LLLAQTEDYVEYSRHGAVIKGQERAVACSKYE
Retrocopy ELLYKXXXXXXXXXXXXXXXSILEKYGGQEHLDAPPAGLLLAQTEDYVEYSRHGAVIKGQERAVACSKYE

Parental  EDVKIHNHTHIWGSYWKEGRWGYKCCHSFFKYSYCTGEAGKETANAEECVISDETGEESVKKPQTLVEMH
          EDVKIHNHTHIWGSYWKEGRWGYKCCHSFFKYSYCTGEAGKETANA.ECVISDETG.ESVKKPQTLVEMH
Retrocopy EDVKIHNHTHIWGSYWKEGRWGYKCCHSFFKYSYCTGEAGKETANAKECVISDETGKESVKKPQTLVEMH

Parental  QEKLKEEKKKKKKKKKHRKSSSDSDDEEKKQEKLKKALNAEEARLLHVKEILQIDERKRPYNSVYETREP
          QEKLKEEKKKK..K.....S.SD..D.EKKQEKLKKALNAE.ARLLHVKEILQID.RKRPYNSVYETREP
Retrocopy QEKLKEEKKKKHRKS---SSESD--DKEKKQEKLKKALNAEKARLLHVKEILQIDKRKRPYNSVYETREP

Parental  TEEEMEAYRMKRQRPDDPMASFLGQQ
          TEEEME.YRMKRQRPDDPMA.FLGQQ
Retrocopy TEEEMETYRMKRQRPDDPMACFLGQQ

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_125 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,