RetrogeneDB ID: retro_dnov_1413

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_19950:17240..18497(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELL2
• Ensembl ID: ENSDNOG00000005103
• Aliases: None
• Description: elongation factor, RNA polymerase II, 2 [Source:HGNC Symbol;Acc:17064]

Sequence

>retro_dnov_1413
ATTGTGGCTGGTGGGTGGAGGGTGGGGGCCCTGCGGGAGGAGCAGCACTATGGGCTGTCATGTGGACAGCTGGGGTGGGG
CATCATCACCATACTGTGTGTAAGGCTCACTGAGACCATGATCCGGGTGCTCGAGACCTACCAGAGCCCCAAGAATTTAA
TTCCTTTCCAACCTTCAGTTCAGTTCCAAGGGCTCTAAGTGCTTGTCAAAATCCCCAAATATGATCCCCCCAATGAAGTG
CACAACTTTAACTTTTATTTGTTAAATATGGATAAACACAACTCTCAAGGCAGCTTTGACTGCATCTGGCAAGCATTTTC
CAGCTCTGGAGCCTCCCAACTCAATTACCTGAGATTTATACAAGATAAAATTATAGTTTGTGCAACAAACGACTCGTAAC
GGATGACAAGAATGACCCAGGCAGAGGAGGAATCCCAAAATCGTAGCACAAGGTTATCAAACCTGGTGGACTATAGGTAG
GGAAAAGAGTGCAAATTTGGAAAGTACCTCAAGCTGTTTCAGATGCAGTGCCTGAGAGTTAAAAGGTCAACTCCCATGAG
CCCTGCAAATACGATTCAAAAGACAGCAGCAGCACTGTTTCTTAGCAGCCATATAGGGACAGACTGATTCACTCACTGGC
AATGAAGGCCTACAAGAAACCTGAGCTGCTTGCTCGATTGCAGAAAGATGGTGTCAATCAAAAAGAGAAGAACTCCCTCG
GAGCAATTCTGCAAAAGGTAGTCATTCTGAATCCTGAAGGCCTGTCATATACCTTAAAGGATTATGTTTTTAAAGAACCT
CAAAGACACTGGCCTGGATACAGTGATATAGACAGACAGTCATTGGAATCAGTGCTCTCTAGAAAACTAAATCCATCTCA
GAATACTGCGGGCACCAGCTGTTCAGAATCTCCCCTATGTTCTAATAGAGATGCTGTGTCTTCTTCTCAGAAACAGCTTT
TGGATTCATATTTCATTGGTCCTTTAATGAATAAAAACCCTCGAATATCTCATCTAACTAATAGAGTACCACCAACATTA
AATGGTCGTTTGAATCCTACCAGTGAAAAGTCTGCTGCAAATTTCCTGCTCACCGCCTGCAGCTTCTACCATTCCTGTCC
GTCCACCGCTGCCGCCAGCATACCTCCCTTTCTCAAATCCTCCTTAGACTGTAAATTCTAACTCCAATTACCCTAGCACT
CCAGAAGGCTGGGGGACTCAAGACCTACCTGTTGACAATTTTAATTAAAATGGTAGT

Alignment

ORF - retro_dnov_1413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76. %
• Parental protein coverage: 65.78 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAGG--AAGLREEQRYGLSCGRLGQDHITVLHVKLTETAIRALETYQSHKNLIPFRPSIQFQGLQGRVK
          ..AGG.....LREEQ.YGLSCG.LG...IT.L.V.LTET.IR.LETYQS.KNLIPF.PS.QFQGL...VK
Retrocopy IVAGGWRVGALREEQHYGLSCGQLGWGIITILCVRLTETMIRVLETYQSPKNLIPFQPSVQFQGL*VLVK

Parental  IPKYDPPNEVHNFNFYLSNVGKDNPQGSFDCIQQTFSSSGASQLNCLGFIQDKITVCATNDSYQMTRERM
          IPKYDPPNEVHNFNFYL.N..K.N.QGSFDCI.Q.FSSSGASQLN.L.FIQDKI.VCATNDS..MTR..M
Retrocopy IPKYDPPNEVHNFNFYLLNMDKHNSQGSFDCIWQAFSSSGASQLNYLRFIQDKIIVCATNDS*RMTR--M

Parental  TQAEEESRNRST-KVIKPGGPYVGKRVQIRKAPQAVSDAVPERKRSTPMNPANTIRKTHSSSSVSQRPYR
          TQAEEES.NRST.KVIKPGG..VGKRVQI.K.PQAVSDAVPE........P.....K..SSS.VS..PYR
Retrocopy TQAEEESQNRST<KVIKPGGL*VGKRVQIWKVPQAVSDAVPES*KVNSHEPCKYDSKD-SSSTVS*QPYR

Parental  DRVIHLLALKAYKKPELLARLQKDGVNQKDKNSLGAILQQVANLNPKDLSYTLKDYVFKELQRDWPGYSD
          DR.IH.LA.KAYKKPELLARLQKDGVNQK.KNSLGAILQ.V..LNP..LSYTLKDYVFKE.QR.WPGYSD
Retrocopy DRLIHSLAMKAYKKPELLARLQKDGVNQKEKNSLGAILQKVVILNPEGLSYTLKDYVFKEPQRHWPGYSD

Parental  IDRRSLESVLSRKLNPSQNTAGTSRSESPLCSSRDTASSPSQKRLLDSDFIDPLMNKKARISHLTNRVPP
          IDR.SLESVLSRKLNPSQNTAGTS.SESPLCS.RD..SS.SQK.LLDS.FI.PLMNK..RISHLTNRVPP
Retrocopy IDRQSLESVLSRKLNPSQNTAGTSCSESPLCSNRDAVSS-SQKQLLDSYFIGPLMNKNPRISHLTNRVPP

Parental  TLNGHLNPTSEKSAASLPL-PPAAAAIPTPPPLPSTHLPVSNPPQTVNSNSNSPSTPEGRGTQDLPVDSF
          TLNG.LNPTSEKSAA...L.PPAA..IP..PPLP...LP.SNPP.TVNSNSN.PSTPEG.GTQDLPVD.F
Retrocopy TLNGRLNPTSEKSAANFLL>PPAASTIPVRPPLPPAYLPFSNPP*TVNSNSNYPSTPEGWGTQDLPVDNF

Parental  SQNGS
          ..NGS
Retrocopy N*NGS

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	0.39 RPM	23.34 RPM
SRP012922_cerebellum	0.14 RPM	5.36 RPM
SRP012922_heart	0.23 RPM	1.62 RPM
SRP012922_kidney	0.00 RPM	12.87 RPM
SRP012922_liver	0.00 RPM	26.78 RPM
SRP012922_lung	0.31 RPM	9.32 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.33 RPM
SRP012922_spleen	0.23 RPM	28.73 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_1413 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010607	1 retrocopy	retro_amel_651,
Dasypus novemcinctus	ENSDNOG00000005103	1 retrocopy	retro_dnov_1413 ,
Equus caballus	ENSECAG00000022933	1 retrocopy	retro_ecab_1092,
Homo sapiens	ENSG00000118985	1 retrocopy	retro_hsap_459,
Nomascus leucogenys	ENSNLEG00000014192	1 retrocopy	retro_nleu_881,
Pongo abelii	ENSPPYG00000015647	1 retrocopy	retro_pabe_1757,
Pan troglodytes	ENSPTRG00000017090	1 retrocopy	retro_ptro_346,