RetrogeneDB ID: retro_dnov_1048

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_14070:11547..12434(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZSCAN4
• Ensembl ID: ENSDNOG00000011483
• Aliases: None
• Description: zinc finger and SCAN domain containing 4 [Source:HGNC Symbol;Acc:23709]

Sequence

>retro_dnov_1048
CCCATACAAGGAACAAATGTCTAGAAGAGAGGTGTGAACTCTAAGTTTCAGTGTTCTCAGCTCAGCCCATATCAAACCAA
CAATGGCTCATTTGAAAAGCAGAAATTAAAAATAATTCTGTAAGGCATTTCACTTGTGGCTGCAGCCAGATAATCACAGC
AAGGAAGAAATTATTTCTCAATTGCTCCTGGAACAGTTAATGATGAATGGATACTGCAAAAACTGGTCCACTTTGAGAGG
GAACTGCAATTCAAGCAGAAGAATCCTGGAGAAACTCATGGAAGATCTGACCAATGATTACATGAGGTCACCTGATTTTG
TCCATGTTCACATGCAGGGACAGGAAGCCCACTTCTCAGAGAATATGACCTTAAGTACTCATCTCATGGGAAAAAATGTC
AGCAGGAATCCCAAGAGTATGAGAACGCCCTTCCATGGCCCCCAAAATATTCCCCTTCAAACAGAACACGCAGGGGAATA
TCAACAGTTCTGTGATATTCCAATCAAGTCAATGACAGTATTACTAATTGAGTCAATCAATTACCTACCCTGGTTATTAT
TCAGGAAGATAATAGCCCTAAGCCTGAAGAGGGGTGTGGAACTTGGGAGAACCTGCATAACTCCAGAAGAGCAGAGCTTG
GCTCCTCTGTATCCCAGAAAGGATCCTTAAGAGGACCTTCTCAAGATGTCCCAGTGGAGGTAGAACCACAGTTTCTTCTC
AGGATAGATCTAGCCAGCTCTAAGCCTGTCCCTACCAAGCAAAGCAATTATAGCACATCCAGACATGGAATAAACCAAGA
AAGTGTCCATAGTTCCCCCAAATCATACAAGTGTGAGAACTATCCCAGGATCACTAGGTACCACTTCAGCTAGATACCTA
CCAGAGA

Alignment

ORF - retro_dnov_1048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.59 %
• Parental protein coverage: 70.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PTQGCDLQRREGNSKFQGPQLSLYQTSNGSFAKQELKRLR-KVFHLWLQPEKHSKEEIISQLILEQLVMN
          P.QG.....R..NSKFQ..QLS.YQT.NGSF.KQ.LK....K.FHLWLQP..HSKEEIISQL.LEQL.MN
Retrocopy PIQGTNV*KRGVNSKFQCSQLSPYQTNNGSFEKQKLKIIL>KAFHLWLQPDNHSKEEIISQLLLEQLMMN

Parental  GYCRNRSILKEKWDSSGRNLEKLVGELNDDCMKSPDFVHVHMQGQEALFSENMPLREVIYLMEQMPAGTP
          GYC.N.S.L.....SS.R.LEKL...L..D.M.SPDFVHVHMQGQEA.FSENM.L.....LM.......P
Retrocopy GYCKNWSTLRGNCNSSRRILEKLMEDLTNDYMRSPDFVHVHMQGQEAHFSENMTLS--THLMGKNVSRNP

Parental  RGESMRTPFQGPQNIPLQTGHGDEYKDDSNIFVKRNQINVNITSQGNQVPY-VVIIQEDDSPKPEEGSGS
          ...SMRTPF.GPQNIPLQT.H..EY.....I..K.....V......N..P..V.I.QED.SPKPEEG.G.
Retrocopy K--SMRTPFHGPQNIPLQTEHAGEYQQFCDIPIK--SMTVLLIESINYLPW<VII-QEDNSPKPEEGCGT

Parental  WKNLHNFRRAELGSPTSQEGSLGESSSQDVPMEVETQFLPRTDQASPKPALTNQSSDGTSRCGINQERVH
          W.NLHN.RRAELGS..SQ.GSL....SQDVP.EVE.QFL.R.D.AS.KP..T.QS...TSR.GINQE.VH
Retrocopy WENLHNSRRAELGSSVSQKGSL-RGPSQDVPVEVEPQFLLRIDLASSKPVPTKQSNYSTSRHGINQESVH

Parental  SPPKSYKCEDCPRIFRF-PSQLEAHQR
          S.PKSYKCE..PRI.R..P.QL...QR
Retrocopy SSPKSYKCENYPRITRY<PLQLDTYQR

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	0.97 RPM	0.00 RPM
SRP012922_cerebellum	1.51 RPM	0.14 RPM
SRP012922_heart	0.23 RPM	0.00 RPM
SRP012922_kidney	0.82 RPM	0.00 RPM
SRP012922_liver	0.62 RPM	0.00 RPM
SRP012922_lung	0.92 RPM	0.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.92 RPM	0.00 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_1048 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005419	2 retrocopies	retro_cpor_1470, retro_cpor_285,
Dasypus novemcinctus	ENSDNOG00000011483	11 retrocopies	retro_dnov_1048 , retro_dnov_1253, retro_dnov_1287, retro_dnov_1505, retro_dnov_174, retro_dnov_1780, retro_dnov_2499, retro_dnov_2556, retro_dnov_2666, retro_dnov_859, retro_dnov_964,
Equus caballus	ENSECAG00000015200	1 retrocopy	retro_ecab_78,
Loxodonta africana	ENSLAFG00000003257	1 retrocopy	retro_lafr_171,
Ictidomys tridecemlineatus	ENSSTOG00000023779	1 retrocopy	retro_itri_408,