RetrogeneDB ID: retro_dnov_1468

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_21014:28623..29303(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMYND19
• Ensembl ID: ENSDNOG00000006644
• Aliases: None
• Description: zinc finger, MYND-type containing 19 [Source:HGNC Symbol;Acc:21146]

Sequence

>retro_dnov_1468
ATGACCGACTTCAAGTTGGGCATCGTGAGGCTCGGCCAGGTGGCCGGAAGACCAAGTATACACTGATAGATGAGCAGGAC
ATCCCGCTGGTGGAGAGCTACTCTTTGGAGGCCCGAATGGAAGTAGATGCAGATGGAAATGGTGCTAAAATCTTTGAATT
ATGCCTTTGACAAAAACTGAGGATGGGAATCAGGACTGCTGCTTCATGAGCTGCTGTGGTCGTGGCACAGGGGAGGCATC
ACGTCCAGCTTCCAAGTGTTGCACCTCAATGCGGTGACCGTGGACAATCGCCTGGACAACCTGCAGCTGGTACAGTGGGG
CTGGTGGTCCAAAGCCGAGGAGACTTCCAGCAAGCAACAGGAGCAAAGCTTGTACTGGCTTGCGATCCAACAGCTCCCCT
CGGACCCCCTGGAGGAGCCGTTCCCTGTCCTGAACGTGGCACGGTACTACAAGCCAATGGGGACGTGGTGGAGGAGGAGG
AGGGCTCTTGCACCTACTACGAGTGTTGCTACCCACCCTACACGGTGATGGAGAAGCAGCTCCATGAGTTCAACATCTGC
AGACGCTGCCAGGTGGCCCGGTACTGTGGCTCCCAGTGCCAGCAGAAGGACTGGCCTGACCACTAGAAGCACTGCCATGA
AAAGAAGTGCCCCTTCCAGCACGAGCTCGAGCTGGAGCGA

Alignment

ORF - retro_dnov_1468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTDFKLGILLLGRVAG-KTKYTLIDEQDIPLVESYSFEARMEVDADGNGAKIFA-YAFDKNRGRGSGRLL
          MTDFKLGI..LG.VAG.KTKYTLIDEQDIPLVESYS.EARMEVDADGNGAKIF..YAFDKN.G..SG.LL
Retrocopy MTDFKLGIVRLGQVAG<KTKYTLIDEQDIPLVESYSLEARMEVDADGNGAKIFE>YAFDKN*GWESGLLL

Parental  HELLWERHRGGIAPGFQVVHLNAVTVDNRLDNLQLVPWGW-PKAEETSSKQREQSLYWLAIQQLPTDPLE
          HELLW..HRGGI...FQV.HLNAVTVDNRLDNLQLV.WGW..KAEETSSKQ.EQSLYWLAIQQLP.DPLE
Retrocopy HELLWSWHRGGITSSFQVLHLNAVTVDNRLDNLQLVQWGWWSKAEETSSKQQEQSLYWLAIQQLPSDPLE

Parental  EQFPVLNVARYYN-ANGDVVEEEEGSCTYYECRYPPCTAMEKQLREFNICGRCQVARYCGSQCQQKDWPA
          E.FPVLNVARYY..ANGDVVEEEEGSCTYYEC.YPP.T.MEKQL.EFNIC.RCQVARYCGSQCQQKDWP.
Retrocopy EPFPVLNVARYYK<ANGDVVEEEEGSCTYYECCYPPYTVMEKQLHEFNICRRCQVARYCGSQCQQKDWPD

Parental  HKKHCREKKRPFQHELEPER
          H.KHC.EKK.PFQHELE.ER
Retrocopy H*KHCHEKKCPFQHELELER

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	0.00 RPM	5.25 RPM
SRP012922_cerebellum	0.14 RPM	6.74 RPM
SRP012922_heart	0.00 RPM	1.86 RPM
SRP012922_kidney	0.00 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	2.01 RPM
SRP012922_lung	0.00 RPM	3.21 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.60 RPM
SRP012922_spleen	0.00 RPM	5.95 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_1468 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006644	2 retrocopies	retro_dnov_1389, retro_dnov_1468 ,
Dipodomys ordii	ENSDORG00000008360	1 retrocopy	retro_dord_390,
Equus caballus	ENSECAG00000012412	1 retrocopy	retro_ecab_903,
Echinops telfairi	ENSETEG00000005023	1 retrocopy	retro_etel_1068,
Homo sapiens	ENSG00000165724	1 retrocopy	retro_hsap_1367,
Gorilla gorilla	ENSGGOG00000006875	1 retrocopy	retro_ggor_1065,
Macropus eugenii	ENSMEUG00000011727	1 retrocopy	retro_meug_2010,
Macaca mulatta	ENSMMUG00000019610	1 retrocopy	retro_mmul_2195,
Monodelphis domestica	ENSMODG00000017172	1 retrocopy	retro_mdom_764,
Mus musculus	ENSMUSG00000026974	3 retrocopies	retro_mmus_1433, retro_mmus_2466, retro_mmus_942,
Nomascus leucogenys	ENSNLEG00000009236	1 retrocopy	retro_nleu_1071,
Tursiops truncatus	ENSTTRG00000010812	1 retrocopy	retro_ttru_900,