RetrogeneDB ID: retro_itri_1007

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393358.1:5958901..5959816(+)
• Located in intron of: ENSSTOG00000002257

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSSTOG00000003046
• Aliases: None
• Description: nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]

Sequence

>retro_itri_1007
GATGGTCTTATAGAACCACCAACAGGATACATTAGAAACTTGCCTAGTGTAGTTAAGAGATGAATGGATACTCTCAAAAG
CCTTCAAGTTCAGTGTGCACAAACAGAAACCAAATTCTGAGGAATTTCTGTGATCTTGAAAAGACCTATGCTGTTCTCTC
TCAGCCTCTATTTGAAAGTGATTTGAGGTCACGAAATGCAATTTATGAAACCACAGAAGAAAAATATGAATGGAAACCAG
GGAAGCAAGAAATATGAGAGAAAATGAAAGAAGAGGTTACAATCAAAATGAGAAAAAGGATGAAGAAAAAGGAGAACCCA
AAGAAATTTCTCAGTTTGGGCTGACTGTTTTAAGGAGTGATAAAATACACAATAATATGGTGCAGGAAAATAACAAACCT
ATTCAAAGCATTGAAAGATAGTAAAGTGAAATTCTCAGATTCTGGCCAGTCTACTTGTTATGTCTTAGAATTTCACTTTG
AACCCAAAGAATATTTCACAAATCAAGTGTTGACAAAGATACACAGAATGAGGTCAGAACCAGATGATTTGAATTCCTTT
TCTTGTAATGGACCAGAAATTATGAGTTGTATAGGATGCCAGGAAGATTGGAAAACAGGAAACAACATCACTTTGGAAAT
CATTAAGCAGCAACAACAAAAACGAACGTAGGCCAGTTTGCACCATGATGATTAAAATGGGTCTCCAGTGACCTTTTTCT
TTTTTCCTTTCCCCTCCTGAAGTTCCTGCAGATGAAGATTCCAATGCTGCTGCTGAAGCTATCCTCGCCAGAGACTTTAA
AACTGGTCCCTTTGTATGTGAACACATAAGCCAAAGATCACTGTTACACTTTCCTGGAGAACCTATTGATGATGGTGATG
ATAGCTGTGATGAAGGAGATAATGAAGGAGAAGAG

Alignment

ORF - retro_itri_1007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.49 %
• Parental protein coverage: 81.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DGLVETPTGYIESLPRVVKRRVNALKNLQVKCAQIEAKF-YEEVHDLERKYAVLYQPLFDKRFEIINAIY
          DGL.E.PTGYI..LP.VVKR....LK.LQV.CAQ.E.KF......DLE..YAVL.QPLF.......NAIY
Retrocopy DGLIEPPTGYIRNLPSVVKR*MDTLKSLQVQCAQTETKF<LRNFCDLEKTYAVLSQPLFESDLRSRNAIY

Parental  EPTEEECEWKPDEEEEISEELKEKAKI-EDEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPI-L
          E.TEE..EWKP....EI.E..KE...I...EKKDEEK..PK.I..F.LTV.........MVQE...PI..
Retrocopy ETTEEKYEWKPG-KQEI*EKMKEEVTI<QNEKKDEEKGEPKEISQFGLTVLRSDKIHNNMVQENNKPI<S

Parental  KH-LKDIKVKFSDAGQPMEFILEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDW
          KH.LKD.KVKFSD.GQ.....LEFHFEP.EYFTN.VLTK..RMRSEPDD...FS..GPEIM.C.GCQ.DW
Retrocopy KH<LKDSKVKFSDSGQSTCYVLEFHFEPKEYFTNQVLTKIHRMRSEPDDLNSFSCNGPEIMSCIGCQEDW

Parental  KKGKNVTLKTIKKKQ-KHKGRGTVRTVTKTVSNDSFFNFFAPPEVPDSGDLDDDAEAILAADFEIGHFLR
          K.G.N.TL..IK..Q.K...R.......K......F..F..PPEVP...D....AEAILA.DF..G.F..
Retrocopy KTGNNITLEIIKQQQ>KNERRPVCTMMIKMGLQ*PFSFFLSPPEVPADEDSNAAAEAILARDFKTGPFVC

Parental  ERIIPRSVLYFTGEAIEDDDDDYDEEGEEADE
          E.I..RS.L.F.GE.I.D.DD..DE...E..E
Retrocopy EHISQRSLLHFPGEPIDDGDDSCDEGDNEGEE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1007 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1007 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Otolemur garnettii	ENSOGAG00000010319	4 retrocopies	retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pteropus vampyrus	ENSPVAG00000016032	2 retrocopies	retro_pvam_1282, retro_pvam_306,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Ictidomys tridecemlineatus	ENSSTOG00000003046	2 retrocopies	retro_itri_1007 , retro_itri_416,