RetrogeneDB ID: retro_dord_576

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_35239:10902..11244(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hrsp12
• Ensembl ID: ENSDORG00000015382
• Aliases: None
• Description: heat-responsive protein 12 [Source:MGI Symbol;Acc:MGI:1095401]

Sequence

>retro_dord_576
ATGTCGTCTCTAATCTGAAAGGTGATCAGCACCGCGAAAAGCCCCAGGCCCATTGGTCCCTACAGTCAAGCTGTGTTAGT
CAACCGGACTGTGTACGTTTCAGGGCAGGTAGGCCTGGACCCTTCAAGTGGAAAGCTTGTGCCAGGAGGGGTGGCGGAAG
AAACAAAACAAGCTCTTACAAACATTATTGAAATTTTGAAAGCAGCAGGCTGTGACTTCACCAATGTGGTAAAAGCAACC
ATCTTTCTGACTGACATGAATGACTTTGGTACTGTCAATGAAGTCTACAAACAATTTTTCAAGAGTGATTTTCCAGCTCG
ATCTGCCTTACCCATAGGAGCC

Alignment

ORF - retro_dord_576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.09 %
• Parental protein coverage: 83.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSLIRKVITAAKNPRPIGPYSHAVLVDRTMYISGQVGLDPSSGKLVPGGVAEEAKQALTNMFEILKAAG
          MSSLI.KVI..AK.PRPIGPYS.AVLV.RT.Y.SGQVGLDPSSGKLVPGGVAEE.KQALTN..EILKAAG
Retrocopy MSSLI*KVISTAKSPRPIGPYSQAVLVNRTVYVSGQVGLDPSSGKLVPGGVAEETKQALTNIIEILKAAG

Parental  CDFTNVVKTTVFLTDMNDFGTVNEVYKQFFKSDFPARSAYQVAA
          CDFTNVVK.T.FLTDMNDFGTVNEVYKQFFKSDFPARSA....A
Retrocopy CDFTNVVKATIFLTDMNDFGTVNEVYKQFFKSDFPARSALPIGA

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_576 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 12 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030250	1 retrocopy	retro_cfam_668,
Choloepus hoffmanni	ENSCHOG00000001278	8 retrocopies	retro_chof_133, retro_chof_1972, retro_chof_2434, retro_chof_2503, retro_chof_2676, retro_chof_380, retro_chof_515, retro_chof_757,
Callithrix jacchus	ENSCJAG00000015560	2 retrocopies	retro_cjac_1702, retro_cjac_465,
Dasypus novemcinctus	ENSDNOG00000025138	3 retrocopies	retro_dnov_1155, retro_dnov_224, retro_dnov_793,
Dipodomys ordii	ENSDORG00000015382	2 retrocopies	retro_dord_576 , retro_dord_713,
Gorilla gorilla	ENSGGOG00000001185	1 retrocopy	retro_ggor_1153,
Loxodonta africana	ENSLAFG00000002078	1 retrocopy	retro_lafr_437,
Macaca mulatta	ENSMMUG00000011825	2 retrocopies	retro_mmul_558, retro_mmul_88,
Monodelphis domestica	ENSMODG00000006575	1 retrocopy	retro_mdom_319,
Ornithorhynchus anatinus	ENSOANG00000021532	1 retrocopy	retro_oana_33,
Otolemur garnettii	ENSOGAG00000001465	3 retrocopies	retro_ogar_2308, retro_ogar_2951, retro_ogar_552,
Ictidomys tridecemlineatus	ENSSTOG00000011452	4 retrocopies	retro_itri_1591, retro_itri_192, retro_itri_605, retro_itri_894,