RetrogeneDB ID: retro_dord_485

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_22593:18837..19400(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc59
• Ensembl ID: ENSDORG00000003005
• Aliases: None
• Description: coiled-coil domain containing 59 [Source:MGI Symbol;Acc:MGI:1289302]

Sequence

>retro_dord_485
CAAGGCTTTTCATTTTGGAGAAAACTGAAGATTCAGAAATACTACAGGAAATTGAAGTGGAAGGGCAAGACGGGTCAAAC
GTCCCAGGAATCCTAGTTCACAGATCACTACTCAGATCATCTGAACCATCTCTATCTGGCTGAAGAAGAAAGGTTCAGGA
AGCAACAAAGAAGAGTTGGCCATCATTTGCCAAAATCAGCAGCTGACCAGACTTTGCCTGAAGAGCAACACTCTAACACT
GACCAGACTTTGCCCGACGACCAATGTGGTCGTGTTCACCAGCTTCTGCCAGAAGAGCAAGACAGCCAAACAGTAAATTC
CGTGACTGTTCCAAAGAAAAGTAAAAAGAAAACCTCAAATCAGAAAACAAAAGAAGAATATAAACAAATAGAAGCTAAGT
GTGCTGCTAAGAAACAAGAATTTGAGAGGAGGAAATGAGAAAGAAGCCCTAATGACAGTACCAAAAAAAAATTGGAAATA
TTCAAAATATTGAGCAAAAAGACTAAAAAGGGACACCAAATTTGAATTTACAAATGGAATATCTTCTTCAAAAACTACAG
GAA

Alignment

ORF - retro_dord_485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.59 %
• Parental protein coverage: 98.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QGFAFRRKLKIQKYYRKLQWKEKKGQTSHESQFTDHYPDHLKHLYLAEEERLRKQQRRVGQHLPESATDQ
          QGF.F.RKLKIQKYYRKL.WK.K.GQTS.ES.FTDHY.DHL.HLYLAEEER.RKQQRRVG.HLP.SA.DQ
Retrocopy QGFSFWRKLKIQKYYRKLKWKGKTGQTSQES*FTDHYSDHLNHLYLAEEERFRKQQRRVGHHLPKSAADQ

Parental  PLPEE-HSNTDQTLVEDQYCGVHQLRPEEQDSQTVNSVTIPKKNKKKTSNQKAKEEYEQIQAKRAAKKQE
          .LPEE.HSNTDQTL..DQ...VHQL.PEEQDSQTVNSVT...................QI.AK.AAKKQE
Retrocopy TLPEEQHSNTDQTLPDDQCGRVHQLLPEEQDSQTVNSVTVXXXXXXXXXXXXXXXXXKQIEAKCAAKKQE

Parental  FERRKQEREEAQRQYKKKKMEMFKILSKKTKKGQ-PNLNLQMEYLLQKIQE
          FERRK...E...........E.FKILSKKTKKG..PNLNLQMEYLLQK.QE
Retrocopy FERRK*--ERSPNDSTXXXLEIFKILSKKTKKGH<PNLNLQMEYLLQKLQE

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_485 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016875	1 retrocopy	retro_amel_954,
Bos taurus	ENSBTAG00000036282	4 retrocopies	retro_btau_725, retro_btau_726, retro_btau_727, retro_btau_728,
Choloepus hoffmanni	ENSCHOG00000007788	1 retrocopy	retro_chof_1648,
Dasypus novemcinctus	ENSDNOG00000011546	1 retrocopy	retro_dnov_1033,
Dipodomys ordii	ENSDORG00000003005	1 retrocopy	retro_dord_485 ,
Echinops telfairi	ENSETEG00000000256	2 retrocopies	retro_etel_1338, retro_etel_1789,
Gorilla gorilla	ENSGGOG00000025296	2 retrocopies	retro_ggor_1386, retro_ggor_99,
Microcebus murinus	ENSMICG00000000967	4 retrocopies	retro_mmur_1456, retro_mmur_354, retro_mmur_689, retro_mmur_909,
Oryctolagus cuniculus	ENSOCUG00000017824	2 retrocopies	retro_ocun_1782, retro_ocun_498,
Otolemur garnettii	ENSOGAG00000004383	1 retrocopy	retro_ogar_2065,
Pan troglodytes	ENSPTRG00000005266	1 retrocopy	retro_ptro_1270,
Tupaia belangeri	ENSTBEG00000008887	7 retrocopies	retro_tbel_1515, retro_tbel_2047, retro_tbel_2126, retro_tbel_302, retro_tbel_3391, retro_tbel_3721, retro_tbel_972,