RetrogeneDB ID: retro_ocun_412

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:172591853..172592716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPM1
• Ensembl ID: ENSOCUG00000011117
• Aliases: None
• Description: nucleophosmin [Source:RefSeq peptide;Acc:NP_001164790]

Sequence

>retro_ocun_412
AATGCAATGGATGTGGACATGAGCCCCCTGAGGCCCCATAACTATCTTTTCAATTGTGAACCAAAGTCTGACAAAAAGTG
AACACAGGAAGTGGACAGATGTGAGTGCCAGTTATCTTTAAGAATGTGCCGTTTTGGTGCTGGTGCAAAGGACGAATCGC
ACGTGGTTGAAACAGAGACAATGGACTGGGAAGACTGTCCGCTTACAGTAACACTGGCAGCTCTGAAAATGCCTGCAAGG
CCCATGGTTTCCCGTGGGGGCTCTGATTTGATGCCTCCTGTGGTCTGCAGCCTGAAGTGGGGGTCAGGGCCTGTGCATGT
TAGTGGCCGCACTCAGTAGCCGTGGGGGGAGATGTGGAGTCAGACGATGGCGAGGGGAAGGACGTGAAGCTATTAAATAT
ATCCAGAAACTGATCTGCCCCAGAGGTGGCGGCAAGGTACCGCAAGACAAAGCAAAGCTTGCTGCTGCTGAAGACAACGG
AGAAGATGATGAAGATGAAGATGAAGATGAAGATGATGATTTGGATGAGGAGGAGACTGAACAAAAACCTCCAGTGAACA
AATCTACGTGAGATACCGCAGGCAAAAAGAGACAAAAATCAAACCAAAATGGAAAAGACTCAAAACCATCAACACCAAGA
TCAAAAGGTCCAGAACCCTTCAAAGAGCAGGGGAAAAAAAAAAAAAACCTCCTAAAACATCACAAATACCTAGCTTTGTA
GTCGACTTTAAAGTAAAAATGCAAGCCAGTATAGGAAGGGGTGGTTCTCTTCCCAAAGTGGAAGCCAAGTTCATCTATTA
TGTGAAGAACCCTTCTGGATGTCTGAGCAGGAGGCTATTCAGGATCTCTGGCAGTGGAGGAGG

Alignment

ORF - retro_ocun_412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.69 %
• Parental protein coverage: 98.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DSMDMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPI
          ..MD.DMSPLRP.NYLF.CE.K.DK.....VD..E...QLSLR....GAGAKDE.H.VE.E.M..E..P.
Retrocopy NAMDVDMSPLRPHNYLFNCEPKSDKK*TQEVDRCEC--QLSLRMCRFGAGAKDESHVVETETMDWEDCPL

Parental  KVTLATLKMSVQPTVSLGGFEITPPVVFIVSSSENPMIMSDN-FILAVEEDAESEDEEEEDVKLLSISGK
          .VTLA.LKM...P.VS.GG....PPVV........P...S......AV..D.ES.D.E..DVKLL.IS..
Retrocopy TVTLAALKMPARPMVSRGGSDLMPPVVCSLKWGSGPVHVSGR<HSVAVGGDVESDDGEGKDVKLLNISRN

Parental  RSAPG-GGSKVPQKKVKLAAEEEKDGKGMAQDRFDDDDDFDDEETEEKAPVKKSIRDTPAKNAQK---SN
          .SAP..GG.KVPQ.K.KLAA.E...G..............D.EETE.K.PV.KS..DT..K..QK.....
Retrocopy *SAPE<GGGKVPQDKAKLAAAED-NGXXXXXXXXXXXXXLDEEETEQKPPVNKST*DTAGKKRQKSNQNG

Parental  QNGKDSKPSTP-RSKG-QESFKKQEKTPKTPKGPTSVEDIKAKMQASIEKGGSLPKVEAKFINYVKN-CF
          ...K.S.P....RS...Q....K..K.PKT...P..V.D.K.KMQASI..GGSLPKVEAKFI.YVKN..F
Retrocopy KDSKPSTPRSK<RSRTLQRAGEKKKKPPKTSQIPSFVVDFKVKMQASIGRGGSLPKVEAKFIYYVKN<PF

Parental  RMTDQEAIQDLWQWRK
          .M..QEAIQDLWQWR.
Retrocopy WMSEQEAIQDLWQWRR

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
SRP017611_brain	0.00 RPM	31.79 RPM
SRP017611_kidney	0.00 RPM	47.13 RPM
SRP017611_liver	0.00 RPM	16.03 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_412 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_412 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019334	13 retrocopies	retro_cjac_1559, retro_cjac_1682, retro_cjac_1696, retro_cjac_1733, retro_cjac_2075, retro_cjac_2351, retro_cjac_2368, retro_cjac_2533, retro_cjac_2605, retro_cjac_3270, retro_cjac_3416, retro_cjac_4117, retro_cjac_838,
Mus musculus	ENSMUSG00000057113	5 retrocopies	retro_mmus_1301, retro_mmus_1798, retro_mmus_3131, retro_mmus_539, retro_mmus_550,
Oryctolagus cuniculus	ENSOCUG00000011117	1 retrocopy	retro_ocun_412 ,