RetrogeneDB ID: retro_dord_692

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5647:56075..56817(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Stk16
• Ensembl ID: ENSDORG00000000152
• Aliases: None
• Description: serine/threonine kinase 16 [Source:MGI Symbol;Acc:MGI:1313271]

Sequence

>retro_dord_692
GAAGGGCAGGACTGGGAAGAGGCCCAGAGAGAAGCAAACGTGCATGGCCCCAACATCCTTCACCTCATGGCTTACTCTCT
GAGAGAGCAGGGTGCTAAGTATGAGGCCTGGCTGCTGCTACCTTTCTTCAAGAGAGGTACACTGTGGAATGAAATAGAAA
GGCTGAAGGACCAAGGCAATTTCCTGACTGAGGATCAAATCCTTCGGCTGTACCTTGGGTATCTGCAGAGGCTTGGAGGC
CATTCATGCCAAAGGTTACGTTCACAGGGACCTGATGCCCACCAATATTTTGCTTGGAGATGAGGAGCAGCCAGTTTTAA
TGGACTTAGGTTCTATGAATCAAGCATGTATTCATGTGGAGAGCTCCCGACAGGCCCTAGCGCTGCAAAACTGGGCAGCA
CAGAGGTGCACCATCTCCTACCGGGCCCCAGAACTCTTCTCTGTGCAGAGCTACTGTGTCATTGATGAGCGGACTGATGT
GTGGTCTCTAGGTTGTGTGCTTTCTGCCATGATGTTTGGGGAAGGCCCTTATGACATGGTGTTCCAGAAGGGTGGCAGTG
TGGCTCTTGCTCTTCAGAACCAACTCAACATCCCACAAAGTCGCAGGCATTCTTCAGCCCTGCAGTAGCTGCTAACCTCC
ATGATGACTGTGGACCCCCAACAACGCCCTCACGTTCCTCTTCTCCTCAGTCAGTTGGAGGTACTGCCGCCTCCAACTCT
TGACCACTCAAATATGAACATA

Alignment

ORF - retro_dord_692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.7 %
• Parental protein coverage: 82.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQQDREEAQREANMHRLFHHPNILHLMAYSLRERGAKYEAWLLLPFFKRGTLWNEIERLKDQGNFLTEDQ
          E.QD.EEAQREAN.....H.PNILHLMAYSLRE.GAKYEAWLLLPFFKRGTLWNEIERLKDQGNFLTEDQ
Retrocopy EGQDWEEAQREANV----HGPNILHLMAYSLREQGAKYEAWLLLPFFKRGTLWNEIERLKDQGNFLTEDQ

Parental  ILRLLLG-ICRGLEAIHAKGYAHRDLKPTNILLGDEEQPVLMDLGSMNQACIHVEGSRQALALQDWAAQR
          ILRL.LG.ICRGLEAIHAKGY.HRDL.PTNILLGDEEQPVLMDLGSMNQACIHVE.SRQALALQ.WAAQR
Retrocopy ILRLYLG>ICRGLEAIHAKGYVHRDLMPTNILLGDEEQPVLMDLGSMNQACIHVESSRQALALQNWAAQR

Parental  CTISYRAPELFSVQSYCVIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLNIPQSPRHSP
          CTISYRAPELFSVQSYCVIDERTDVWSLGCVL.AMMFGEGPYDMVFQKG.SVALA.QNQLNIPQS.RHS.
Retrocopy CTISYRAPELFSVQSYCVIDERTDVWSLGCVLSAMMFGEGPYDMVFQKGGSVALALQNQLNIPQSRRHSS

Parental  ALRQLLTSMMTVDPQQRPHIPLLLSQLEALQPPTLGQHTTQI
          AL..LLTSMMTVDPQQRPH.PLLLSQLE.L.PPTL......I
Retrocopy ALQ*LLTSMMTVDPQQRPHVPLLLSQLEVLPPPTLDHSNMNI

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_692 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000152	1 retrocopy	retro_dord_692 ,
Equus caballus	ENSECAG00000014093	1 retrocopy	retro_ecab_166,
Homo sapiens	ENSG00000115661	1 retrocopy	retro_hsap_1334,
Gorilla gorilla	ENSGGOG00000010907	1 retrocopy	retro_ggor_1040,
Macropus eugenii	ENSMEUG00000006422	1 retrocopy	retro_meug_1579,
Myotis lucifugus	ENSMLUG00000008066	1 retrocopy	retro_mluc_1213,
Pongo abelii	ENSPPYG00000013202	1 retrocopy	retro_pabe_1108,
Pan troglodytes	ENSPTRG00000012948	1 retrocopy	retro_ptro_911,
Ictidomys tridecemlineatus	ENSSTOG00000025197	2 retrocopies	retro_itri_1662, retro_itri_602,