RetrogeneDB ID: retro_dnov_2029

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_43071:5437..6272(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IGBP1
• Ensembl ID: ENSDNOG00000014731
• Aliases: None
• Description: immunoglobulin (CD79A) binding protein 1 [Source:HGNC Symbol;Acc:5461]

Sequence

>retro_dnov_2029
AGCAGGTTTGATTTATTCAGCTGAAATGAAGACTTGGAAGAGATGGCTTCCACCGACCTGAAGGACCCAATGGTGCCAGC
ATTTCAAGGAGCTGTCGCCATGAAACAAGCCAGTCCCAGCAAGCAGCTAGATCATTTGCAGCAGGCTTGAGAACACTTTC
TAAACTACTTACCTCCGTGTCATTACTATCATGTGGTTGAATTAGAACTGCCCCAAACCAGGAACAACTCGGCTGAAAAT
AACACCGCTAGCTCCTCCACGGCCTATGCTAGCCCCGTTGCTATGGCATCTTGAAGACAGGCTGAAATAGAGAGGTACAA
GCGCAAGAAGGAGGTGAACATAGATTACCTGCAATGAAACCTTCTGTGGAAAATTATCAAGCAGACGATGAGTGTGTTTG
TGAATATCATCTCTTTCACGTTGAGAGGTACATTGCTATCAGCTTGGAAGAGATTGAAAGTATTGTTCAGGAAATAAAGA
TTCTGAGAGAAAAAGACTTCTCAAAAGAGGCATCGGTTTCTTGCTCATCTTGTCAGGAGAGGCCTCCAACGAAGCCCTTC
ATTCTCACTTGGGACATGGCCCAAGCCAAAGCTGGTTATCCAAGTCTGGTGACCATGACAGAGAATGGCTAGAATGATCA
ACATCAGAAATATGGAGCATCACCAAATCAAGGAACAGCCAAGACAACACCGGAGTCCAAAAAAGCAGCTCAACAGCAGG
AAATCAGGAGCAGAAGGAGGAAGACACTGATGCAAAGACACTGCACGGAGCTTGGGGGCGGGATGACCCTAAGGACACCC
ATCCTAGGGGTTACGGCAACCGACAGAACGTGGGT

Alignment

ORF - retro_dnov_2029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.28 %
• Parental protein coverage: 83.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SQLDLFSRNEDLEEIASTDVKYLMVPAFQGALTMKQVNPSKRLDHLQRAREHFLNYLTQCHYYHVAEFEI
          S..DLFS.NEDLEE.ASTD.K..MVPAFQGA..MKQ..PSK.LDHLQ.A.EHFLNYL..CHYYHV.E.E.
Retrocopy SRFDLFS*NEDLEEMASTDLKDPMVPAFQGAVAMKQASPSKQLDHLQQA*EHFLNYLPPCHYYHVVELEL

Parental  PKTKNNSTENNTASSSMAYPSLVAMASQRQAKVERYKQKKEL-EHRLSALKSSVENGQADDERVREYYLL
          P.T.NNS.ENNTASSS.AY.S.VAMAS.RQA..ERYK.KKE..EHRL.A.K.SVEN.QADDE.V.EY.L.
Retrocopy PQTRNNSAENNTASSSTAYASPVAMAS*RQAEIERYKRKKEV<EHRLPAMKPSVENYQADDECVCEYHLF

Parental  HLQRWIGVSLEEIESIDQEMKILREKDFSKEASTSRSSRQDRPPVKPFILTRDVAQAKVFGAGYPSLATM
          H..R.I..SLEEIESI.QE.KILREKDFSKEAS.S.SS.Q.RPP.KPFILT.D.AQAK...AGYPSL.TM
Retrocopy HVERYIAISLEEIESIVQEIKILREKDFSKEASVSCSSCQERPPTKPFILTWDMAQAK---AGYPSLVTM

Parental  TVDDWYDQHRKYGALPDQGIAKATPAEFKKAAQQQE-DQEQKEEDADEKTLHRAREWDDWKDTHPRGYGN
          T.....DQH.KYGA.P.QG.AK.TP.E.KKAAQQQE..QEQKEED.D.KTLH.A...DD.KDTHPRGYGN
Retrocopy TENG*NDQHQKYGASPNQGTAKTTP-ESKKAAQQQE<NQEQKEEDTDAKTLHGAWGRDDPKDTHPRGYGN

Parental  RQNMG
          RQN.G
Retrocopy RQNVG

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	19.84 RPM
SRP012922_cerebellum	0.00 RPM	19.25 RPM
SRP012922_heart	0.00 RPM	6.73 RPM
SRP012922_kidney	0.00 RPM	18.34 RPM
SRP012922_liver	0.00 RPM	11.46 RPM
SRP012922_lung	0.00 RPM	14.36 RPM
SRP012922_quadricep_muscle	0.17 RPM	19.56 RPM
SRP012922_spleen	0.00 RPM	13.28 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_2029 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 19 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007797	1 retrocopy	retro_btau_215,
Choloepus hoffmanni	ENSCHOG00000013654	3 retrocopies	retro_chof_1523, retro_chof_2206, retro_chof_438,
Callithrix jacchus	ENSCJAG00000012525	6 retrocopies	retro_cjac_111, retro_cjac_1225, retro_cjac_2278, retro_cjac_2968, retro_cjac_3417, retro_cjac_47,
Cavia porcellus	ENSCPOG00000010797	1 retrocopy	retro_cpor_44,
Dasypus novemcinctus	ENSDNOG00000014731	5 retrocopies	retro_dnov_1160, retro_dnov_2029 , retro_dnov_2340, retro_dnov_2380, retro_dnov_678,
Echinops telfairi	ENSETEG00000003397	1 retrocopy	retro_etel_1637,
Felis catus	ENSFCAG00000029688	1 retrocopy	retro_fcat_23,
Homo sapiens	ENSG00000089289	5 retrocopies	retro_hsap_1317, retro_hsap_1848, retro_hsap_2766, retro_hsap_2919, retro_hsap_3059,
Gorilla gorilla	ENSGGOG00000027795	2 retrocopies	retro_ggor_112, retro_ggor_2020,
Myotis lucifugus	ENSMLUG00000004179	1 retrocopy	retro_mluc_316,
Macaca mulatta	ENSMMUG00000013929	2 retrocopies	retro_mmul_1545, retro_mmul_31,
Mus musculus	ENSMUSG00000031221	1 retrocopy	retro_mmus_169,
Nomascus leucogenys	ENSNLEG00000000747	5 retrocopies	retro_nleu_1399, retro_nleu_1653, retro_nleu_2334, retro_nleu_671, retro_nleu_828,
Otolemur garnettii	ENSOGAG00000011797	1 retrocopy	retro_ogar_110,
Pongo abelii	ENSPPYG00000020435	4 retrocopies	retro_pabe_1099, retro_pabe_1451, retro_pabe_2245, retro_pabe_2533,
Pan troglodytes	ENSPTRG00000021990	5 retrocopies	retro_ptro_1233, retro_ptro_1873, retro_ptro_1973, retro_ptro_1982, retro_ptro_901,
Pteropus vampyrus	ENSPVAG00000005483	1 retrocopy	retro_pvam_1462,
Rattus norvegicus	ENSRNOG00000026267	1 retrocopy	retro_rnor_311,
Tarsius syrichta	ENSTSYG00000006214	2 retrocopies	retro_tsyr_1537, retro_tsyr_2131,