RetrogeneDB ID: retro_itri_36

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393302.1:10232334..10233438(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021400
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NSMCE4A
• Ensembl ID: ENSSTOG00000011112
• Aliases: None
• Description: non-SMC element 4 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:25935]

Sequence

>retro_itri_36
ATGTCTGATGAGCAAGGTTCCCTGATGGGAGGCGAGGAGCCAGTGGCGACAGGCACCTGCCGTGCGTGCTCCATGAAGCA
GGTGGAGGAGGAGGAGGGGGAGCCGCCAAAGATGGAAGTGGTGGTGGGGGTGGACAGCTGCTCTGACGACCTCAGCTCCG
GGGACCCCGAGCTAGACTGTCACCTCCTGGGTCAGACCGAGGACGAGGAGAAGTGTCGGAACATCCGCAAGCAATACCGG
CAGCTCATCTACAGTGTCCAGCAGAACCGAGAGGACATAGTGAACACGGCCAGCGACTCCTTAACCGAGGCCCTCGAGGA
AGCCAACGTCCTATTTGATGGAGTGAGCCGAACGAGAGAGGCTGCCCTCGATGCCCAGTTTCTTGTTTTGGCTTCTGATT
TGGGTAAAGAAAAAGCAAAGCAGTTAAATTCTGATATGAGCTTTTTTAATCAAGTAGCGTTTTGTGACTTTCTGTTTGTA
TTTGTGGGCCTCAATTGGATGGAAGACGAATGTGATGAGTTGAGTGGTTGTGATGACAGTATCTCTCTTTCCTTTTGGGA
GACAGTACAGAAGGAAGCAACATCCTGGATATTGCAAGCTGAAACATTCCACTTTATTTTTGGTTCATTCAAGTCTGAGC
CTTTTGTACGAAAGCCCCGACTTGAACATCACAAAAAATTTCGCAAAATGGAAGGAAATGGGGATATGCCTACAAAGTTG
AGGAAGTTGGACCTGAGTACCAACCAAGAAGCAACAGAAAAAGAAGTAGAAAGAATCTTGGGATTGTTGCAAACCTACTT
TCGAAAGTATCCTGATACTCCTGTGTCCTATTTTGAGTTTGTGATTGATCCAAACTCTTTCTCTCGTACAGTGGAGAATA
TATTCTACGTTTCTTTTATTATAAGAGATGGCTTTGCAAGAATAAGGCTTGACCAAGACAGGCTGCCAATATTAGAGCCA
ATTAATATTAACCAAATGGGTGAAGGAGGTGATCCCAGTTCCTTTGGTAGGAAGCAAGGAGTTATATCTCTGAGTTTACA
GGATTGGAAAAATATTGTGGCAACTTTTGAAATTTCAGAGGCTATGATTACAAACTCATATTAG

Alignment

ORF - retro_itri_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.28 %
• Parental protein coverage: 82.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGDEMVDPASLEAETDHGLCRQIRHQYRALINSVQQNREDILN-ASDKLTEVLEEANTLFNGVSRAREAV
          SGD...D...L....D...CR.IR.QYR.LI.SVQQNREDI.N.ASD.LTE.LEEAN.LF.GVSR.REA.
Retrocopy SGDPELDCHLLGQTEDEEKCRNIRKQYRQLIYSVQQNREDIVNTASDSLTEALEEANVLFDGVSRTREAA

Parental  LDAQFLVLASDLGKEKAKQLRSDLNSFDMLRYVETLLTHMGVNPLEAEELIRDEDSSDFEFIVYDSWKIS
          LDAQFLVLASDLGKEKAKQL.SD...F........L....G.N..E.E....DE.S.....I....W...
Retrocopy LDAQFLVLASDLGKEKAKQLNSDMSFFNQVAFCDFLFVFVGLNWMEDE---CDELSGCDDSISLSFWETV

Parental  GKTAENTFNKTHTFHFLLGSIQGELPVPKPRIDRPRKHHMIEEQRAMPAQLKRMEES-HQEATEKEVERI
          .K.A........TFHF..GS...E..V.KPR.....K....E....MP..L.....S..QEATEKEVERI
Retrocopy QKEATSWILQAETFHFIFGSFKSEPFVRKPRLEHHKKFRKMEGNGDMPTKLRKLDLSTNQEATEKEVERI

Parental  LGLLQTYFREDPDTPMSFFDFVVDPHSFPRTVENIFHVSFIIRDGFARIRLDQDRLPIIEPVNINEESEG
          LGLLQTYFR..PDTP.S.F.FV.DP.SF.RTVENIF.VSFIIRDGFARIRLDQDRLPI.EP.NIN...EG
Retrocopy LGLLQTYFRKYPDTPVSYFEFVIDPNSFSRTVENIFYVSFIIRDGFARIRLDQDRLPILEPININQMGEG

Parental  IDQNTQIRNQGIIALSYRDWEEIVKTFEIAEPVIAS
          .D.....R.QG.I.LS..DW..IV.TFEI.E..I..
Retrocopy GDPSSFGRKQGVISLSLQDWKNIVATFEISEAMITN

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_36 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_36 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 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36 ,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,