RetrogeneDB ID: retro_dord_531

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_27606:15203..15719(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Myl12b
• Ensembl ID: ENSDORG00000007562
• Aliases: None
• Description: myosin, light chain 12B, regulatory [Source:MGI Symbol;Acc:MGI:107494]

Sequence

>retro_dord_531
ATGTCGAGCAAAAAGGCCAAGACCAAGACTACTAAGAAGCGCCCACAGCGTGCAACGTCCAATGTGTTTGCTATGTTTGA
CCAGTCCCAGATCCAGGAATTCAAAGAAGCCTTCAACATGATTGACCAGAACAGAGATGGTTTCAACAACAAGGAAGATT
TGCAGGATATGCTTGCTTCTCTAGGGAAGAATCCTACTGATACATACCTGGATGCCATGATGAATGAGGCTCCAGGCCCC
ATCAACTTCACTATGTTCCTCACCATGTTTGGTGAGAAGTTAAATGGCACAGATCCTGAGGATGTCATCAGAAATGCCCT
CTCTTGCTTTGATGAGGAAGCAACAGGTACCATCCAGGAGGATTACCTGCGGGAGCTGCTGACAACCATGGGCGATCGCT
TCACAGATGAGGATGTGGATGAGCTGTACCAAGAAGCCCCTATTGACAAAAAGGGCAATTTCAATTACATTGAGTTCACA
CGTAACCTCAAACACAGAGCGAAAGACAGAAATGAC

Alignment

ORF - retro_dord_531 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSKKAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGK-PTDAYL
          MSSKKAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGF..KEDL.DMLASLGK.PTD.YL
Retrocopy MSSKKAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFNNKEDLQDMLASLGKNPTDTYL

Parental  DAMMNEAP-PI-FTMFLTMFGEKLNGTDP-DVIRN-FAC-DEEATGTIQEDYLRELLTTMGDRFTDEEVD
          DAMMNEAP.PI.FTMFLTMFGEKLNGTDP.DVIRN...C.DEEATGTIQEDYLRELLTTMGDRFTDE.VD
Retrocopy DAMMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNALSCFDEEATGTIQEDYLRELLTTMGDRFTDEDVD

Parental  ELYREAPIDKKGNFNYIEFTRILKHGAKDKDD
          ELY.EAPIDKKGNFNYIEFTR.LKH.AKD..D
Retrocopy ELYQEAPIDKKGNFNYIEFTRNLKHRAKDRND

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_531 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 18 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012665	1 retrocopy	retro_amel_1847,
Canis familiaris	ENSCAFG00000032168	1 retrocopy	retro_cfam_1224,
Dasypus novemcinctus	ENSDNOG00000007004	2 retrocopies	retro_dnov_463, retro_dnov_953,
Dipodomys ordii	ENSDORG00000007562	1 retrocopy	retro_dord_531 ,
Erinaceus europaeus	ENSEEUG00000006985	1 retrocopy	retro_eeur_311,
Felis catus	ENSFCAG00000022871	1 retrocopy	retro_fcat_2019,
Homo sapiens	ENSG00000118680	4 retrocopies	retro_hsap_1487, retro_hsap_3129, retro_hsap_3451, retro_hsap_3985,
Gorilla gorilla	ENSGGOG00000004051	4 retrocopies	retro_ggor_1139, retro_ggor_1140, retro_ggor_2330, retro_ggor_2675,
Myotis lucifugus	ENSMLUG00000005189	2 retrocopies	retro_mluc_706, retro_mluc_947,
Monodelphis domestica	ENSMODG00000021464	1 retrocopy	retro_mdom_987,
Mustela putorius furo	ENSMPUG00000005011	1 retrocopy	retro_mputfur_294,
Mus musculus	ENSMUSG00000034868	2 retrocopies	retro_mmus_1483, retro_mmus_1539,
Nomascus leucogenys	ENSNLEG00000006907	3 retrocopies	retro_nleu_1709, retro_nleu_1906, retro_nleu_2250,
Otolemur garnettii	ENSOGAG00000029777	2 retrocopies	retro_ogar_2409, retro_ogar_857,
Pongo abelii	ENSPPYG00000009032	3 retrocopies	retro_pabe_1236, retro_pabe_2585, retro_pabe_3026,
Pan troglodytes	ENSPTRG00000009836	4 retrocopies	retro_ptro_1006, retro_ptro_2118, retro_ptro_2340, retro_ptro_2705,
Rattus norvegicus	ENSRNOG00000015733	2 retrocopies	retro_rnor_1614, retro_rnor_2718,
Tarsius syrichta	ENSTSYG00000010418	9 retrocopies	retro_tsyr_1034, retro_tsyr_1265, retro_tsyr_1320, retro_tsyr_1464, retro_tsyr_1961, retro_tsyr_2054, retro_tsyr_277, retro_tsyr_391, retro_tsyr_751,