RetrogeneDB ID: retro_dnov_2259

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_59466:5939..7103(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000006598
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000008718
• Aliases: None
• Description: None

Sequence

>retro_dnov_2259
GCATCTGAGTTATTGAAAAAAATGAATGGGATGCTTCTAAATGGTCACAAAGTATTTGTTAGACAACTTAAGTCTGGAAA
AGAACGAAAAGCAGAACTCGGAGCTAGAGCAAAAGAGTTCACCAATTTTTACATCAAGAATTTTGGAGAAGACATGGATG
ATGAGCACCTTGAGGATCTCTTTGGCAAGTTTGGACCTGCCTTAAGTGTGGAAGTAATGACTGATGAAAGTGGAAAATCC
AAAGGCGTTGGATTTGTGAGCTTTGAAAGGCATGAAGATGCACAGAAAGCTGTGGATGAGATGAATGGAAAGGAGCTCAA
TGGAAAACAAATTCACGTTGGACGAGCTCAGAAAAAAGTGGAACGACAGACAGAACTTAAGCGCAAATTTGAACAGATGA
AGCAAGATAGGATCACCAGATATCAGGGTGTTAACCATTATGTGGAAAATCTTGATGATGGTATTGATGATGAACATCTC
CGGAAAGCGTTTTCTCCATTTGGTACAATCACTAGTGCAAAGATTTTGATGAAGGGTAGTCGCAGCAAAGGGTTTAGTTT
TGTATGTTTCTCCTCCCCAGAAGAAGCCACTAAAGCAGTTACAGAAATGAATGGTAGAATTGTGGCCACCAAGCCATTGT
ATGTAGCTTTAGCACAGTGCAAAGGAGAGCACCAGGCTCACCTCACTAACCAGTATATGCAGAGAATGGCAAGTGTAAGA
GCTGTACCCAACCCTGTAATCAACCCCTACCAGGCAGCACCTCCTTTAGGTTACTTCATGGCAGCTATTCCACAGATTCA
GAACCATGCTGCATACTATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCGCCCTGGACTGCTCAGGGTGCCAGAC
CTCATCCATTCCAAAATATGCCTGGTGCTATTCGCCCAGCCACTCCTAGACCACCATTTAGTACTATGCAACCAGCTTCT
TCACAGGTTCCACGAGTCATGTCAATACAACGTGTTACTAATACATCAACACAGACAATGGATCCACATCCTGCGGCTGC
TGCTGCTGCAGCTACTCCTGCTGTCCGTACCATTCCACAGTATAAATATGCAGTGGGAGTTCGCAATCCACAACATCTTA
ATGCACAGCCACAAGTTACCATGCAGCAGCCTGCTGTTCATGTA

Alignment

ORF - retro_dnov_2259 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.66 %
• Parental protein coverage: 68.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAERAIKMNGMLLNDRKXFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSV
          A.E...KMNGMLLN..K.FV...KS.KER.AELGARAKEFTN.YIKNFGEDMDDE.L.DLFGKFGPALSV
Retrocopy ASELLKKMNGMLLNGHKVFVRQLKSGKERKAELGARAKEFTNFYIKNFGEDMDDEHLEDLFGKFGPALSV

Parental  KVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITR
          .VMTDESGKSKG.GFVSFERHEDAQKAVDEMNGKELNGKQI.VGRAQKKVERQTELKRKFEQMKQDRITR
Retrocopy EVMTDESGKSKGVGFVSFERHEDAQKAVDEMNGKELNGKQIHVGRAQKKVERQTELKRKFEQMKQDRITR

Parental  YQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT
          YQGVN.YV.NLDDGIDDE.LRK.FSPFGTITSAK..M.G.RSKGF.FVCFSSPEEATKAVTEMNGRIVAT
Retrocopy YQGVNHYVENLDDGIDDEHLRKAFSPFGTITSAKILMKGSRSKGFSFVCFSSPEEATKAVTEMNGRIVAT

Parental  KPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQ
          KPLYVALAQ.K.E.QAHLTNQYMQRMASVRAVPNPVINPYQ.APP.GYFMAAIPQ.QN.AAYYPPSQIAQ
Retrocopy KPLYVALAQCKGEHQAHLTNQYMQRMASVRAVPNPVINPYQAAPPLGYFMAAIPQIQNHAAYYPPSQIAQ

Parental  LRPSPRWTAQGAXXXXFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAAAAAA
          LRPSP.WTAQGA....FQNMPGAIRPA.PRPPFSTM.PASSQVPRVMS.QRV.NTSTQTM.P.PAAAAAA
Retrocopy LRPSPPWTAQGARPHPFQNMPGAIRPATPRPPFSTMQPASSQVPRVMSIQRVTNTSTQTMDPHPAAAAAA

Parental  ATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHV
          ATPAVRT.PQYKYA.GVRNP.QHLNAQPQVTMQQPAVHV
Retrocopy ATPAVRTIPQYKYAVGVRNP-QHLNAQPQVTMQQPAVHV

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	49.01 RPM	686.47 RPM
SRP012922_cerebellum	13.33 RPM	187.10 RPM
SRP012922_heart	5.34 RPM	94.44 RPM
SRP012922_kidney	21.08 RPM	326.64 RPM
SRP012922_liver	22.76 RPM	326.33 RPM
SRP012922_lung	43.83 RPM	609.83 RPM
SRP012922_quadricep_muscle	8.65 RPM	144.53 RPM
SRP012922_spleen	70.74 RPM	1051.21 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_2259 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 17 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259 ,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273,