RetrogeneDB ID: retro_dord_506

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_24541:14561..14969(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Clic1
• Ensembl ID: ENSDORG00000016424
• Aliases: None
• Description: chloride intracellular channel 1 [Source:MGI Symbol;Acc:MGI:2148924]

Sequence

>retro_dord_506
GCTGGACTGGACGTATTTGCCAAATTTTCTGCCTACATCAAGAATTCAAACCCAACACTCAATGACAATCTGGAGAAGGG
ACTGCTGAAAGCCTAGAAGATCTTAGACAATTACCTGACATCCTTCCTCCCCTCAAAAGAGGATGAGACCATTGTGGAAG
ATGAGGGCATCTCTCAAAGAAAATTGCTGGACTGCCCTGAGCTCACCCTGGCTGACTGCAAACTGTTGGCAAAGCTCCAC
ATAGTGCAGGTGGTATGTAAGAAATACAGGGGATTCGCCATCCCTGCAACTTTTTGAGGAGTGCATCCGTACTGGATCAA
TGCCTATGCTTAGGAAGAATTTGCCTCCACCTGTCCAGATGACAAAGTGATTGAGTTGGTCTTTGAGCAAGTGGCCAATG
CTCTCAAA

Alignment

ORF - retro_dord_506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.41 %
• Parental protein coverage: 56.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGLDIFAKFSAYIKNSNPALNDNLEKGLLKALKILDNYLTSPLPEEVDETSAEDEGVSQRKFLDGNELTL
          AGLD.FAKFSAYIKNSNP.LNDNLEKGLLKA.KILDNYLTS.LP...DET..EDEG.SQRK.LD..ELTL
Retrocopy AGLDVFAKFSAYIKNSNPTLNDNLEKGLLKA*KILDNYLTSFLPSKEDETIVEDEGISQRKLLDCPELTL

Parental  ADCNLLPKLHIVQVVCKKYRGFTIPEAFRGVHRYLSNAYAREEFASTCPDDEEIELAYEQVAKALK
          ADC.LL.KLHIVQVVCKKYRGF.IP..F.GVH.Y..NAYA.EEFASTCPDD..IEL..EQVA.ALK
Retrocopy ADCKLLAKLHIVQVVCKKYRGFAIPATF*GVHPYWINAYA*EEFASTCPDDKVIELVFEQVANALK

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_506 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 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000621	2 retrocopies	retro_cfam_481, retro_cfam_525,
Callithrix jacchus	ENSCJAG00000002788	1 retrocopy	retro_cjac_2972,
Dipodomys ordii	ENSDORG00000016424	3 retrocopies	retro_dord_506 , retro_dord_524, retro_dord_550,
Felis catus	ENSFCAG00000019049	1 retrocopy	retro_fcat_1301,
Gorilla gorilla	ENSGGOG00000011331	1 retrocopy	retro_ggor_2153,
Macropus eugenii	ENSMEUG00000015201	1 retrocopy	retro_meug_254,
Macaca mulatta	ENSMMUG00000029827	3 retrocopies	retro_mmul_1269, retro_mmul_290, retro_mmul_902,
Monodelphis domestica	ENSMODG00000015240	1 retrocopy	retro_mdom_1166,
Nomascus leucogenys	ENSNLEG00000006264	3 retrocopies	retro_nleu_1296, retro_nleu_24, retro_nleu_2894,
Oryctolagus cuniculus	ENSOCUG00000022545	1 retrocopy	retro_ocun_1449,
Otolemur garnettii	ENSOGAG00000031840	4 retrocopies	retro_ogar_2402, retro_ogar_3273, retro_ogar_407, retro_ogar_982,
Procavia capensis	ENSPCAG00000013268	1 retrocopy	retro_pcap_30,
Pongo abelii	ENSPPYG00000016456	2 retrocopies	retro_pabe_1514, retro_pabe_886,
Pan troglodytes	ENSPTRG00000017982	2 retrocopies	retro_ptro_1238, retro_ptro_724,
Sarcophilus harrisii	ENSSHAG00000006493	1 retrocopy	retro_shar_28,
Tarsius syrichta	ENSTSYG00000001540	2 retrocopies	retro_tsyr_1452, retro_tsyr_722,