RetrogeneDB ID: retro_itri_1290

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393429.1:3116054..3116360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPP19
• Ensembl ID: ENSSTOG00000003677
• Aliases: None
• Description: cAMP-regulated phosphoprotein, 19kDa [Source:HGNC Symbol;Acc:16967]

Sequence

>retro_itri_1290
AGAAGTGAGATTACAGGGAACAACACTATGTCTGTGGAAGTTCCCAAGTAGACTCAGAGGAGTAGCAGAAGGAAATGGAA
GTAACTAATACGAAGAAAGCTGAAAAAGCAAAATTAAAAGGTATTTTTTTTTTACAAAAGCCTGAAGGTTCTGATTTTTT
AAGGAAAACAACTTCAAAAAGGGCAAAAATAATTTGATTCTGGGGATTACAACATGGCTAAAGCAAAGCTGAACAAGCAA
CTTCCCACTGAAACCCTGGAAGGGACAGAGATCACCAATGACCACATTCATACTCCACAGGAGCTA

Alignment

ORF - retro_itri_1290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.39 %
• Parental protein coverage: 74.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRSAAGQNAMSAEVP-EAASAEEQKEMEDKVTSPEKAEEAKLKARYPHLGQKPGGSDFLRK-RLQKGQKY
          R....G.N.MS.EVP....S.E.QKEME..VT...KAE.AKLK.......QKP.GSDFLRK..LQKGQK.
Retrocopy RSEITGNNTMSVEVP<QVDSEE*QKEME--VTNTKKAEKAKLKGXXXX--QKPEGSDFLRK>QLQKGQK*

Parental  FDSGDYNMAKAKMKNKQLPTAAPDKTEVTGDHIPTPQDL
          FDSGDYNMAKAK..NKQLPT.....TE.T.DHI.TPQ.L
Retrocopy FDSGDYNMAKAKL-NKQLPTETLEGTEITNDHIHTPQEL

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_1290 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1290 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 13 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011022	5 retrocopies	retro_btau_1259, retro_btau_1821, retro_btau_1845, retro_btau_952, retro_btau_981,
Canis familiaris	ENSCAFG00000032515	2 retrocopies	retro_cfam_1375, retro_cfam_1402,
Dasypus novemcinctus	ENSDNOG00000004474	9 retrocopies	retro_dnov_1086, retro_dnov_1576, retro_dnov_1960, retro_dnov_2150, retro_dnov_2427, retro_dnov_557, retro_dnov_616, retro_dnov_644, retro_dnov_662,
Dipodomys ordii	ENSDORG00000011321	2 retrocopies	retro_dord_194, retro_dord_33,
Echinops telfairi	ENSETEG00000015550	1 retrocopy	retro_etel_585,
Homo sapiens	ENSG00000128989	2 retrocopies	retro_hsap_2130, retro_hsap_3280,
Gorilla gorilla	ENSGGOG00000025250	1 retrocopy	retro_ggor_198,
Otolemur garnettii	ENSOGAG00000013865	1 retrocopy	retro_ogar_591,
Pongo abelii	ENSPPYG00000006487	2 retrocopies	retro_pabe_120, retro_pabe_1923,
Pan troglodytes	ENSPTRG00000042183	1 retrocopy	retro_ptro_1559,
Sus scrofa	ENSSSCG00000004618	1 retrocopy	retro_sscr_603,
Ictidomys tridecemlineatus	ENSSTOG00000003677	7 retrocopies	retro_itri_1075, retro_itri_1290 , retro_itri_1339, retro_itri_1643, retro_itri_1657, retro_itri_1865, retro_itri_594,
Tursiops truncatus	ENSTTRG00000004804	1 retrocopy	retro_ttru_172,