RetrogeneDB ID: retro_itri_93

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393361.1:4086743..4088006(-)
• Located in intron of: ENSSTOG00000004230

Retrocopy information

• Ensembl ID: ENSSTOG00000004248
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDI2
• Ensembl ID: ENSSTOG00000019447
• Aliases: None
• Description: DNA-damage inducible 1 homolog 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:24578]

Sequence

>retro_itri_93
ATGCTGATCACTGTGTACTGTGTGCGAAGGGACCTCTCTGAGGCAACCTTCTCCCTCCAGGTCAGCCCTGACTTTGAGCT
TTGCAACTTTCGGGTCCTTTGTGAGCTTGAGTCTGGAGTCCCCGTCGACGAGATCCAGATTTTCCACATGGAGCGAATCT
TGGCAGACGATCACTATTCCCTGGGCTCTTATGGCCTCAAAGACGGCGATGTGGTTGTTTTACTTCAAAAGGATAATGTG
GGATCTCGGCCTGTAGGACGGACCCCAAACCAGCCCCGAGTCGATTTTGGTGGGACTGCAGTGCCTGGGACTTCAAACTC
TAGGCAACAGCACCAACACCAGCACCAGCACCAGCACCAGCACCAGCACCAGCACCAACACCAGCACCAGCACCAGCATC
AGAAACGTGCATCCTCTGTACAGCAGTCCCATGGCTTGGCCTCTGGAGAGAAGATGACTTCTTCTCAAGGTCTGGACAGC
CCCACTTTAATTCGCAGTATGCTGCTTTCCAGTCCTCATGATCTGTCCCTGCTGAAGGAACGCAACCCAACCTTGGCGGA
AGCACTGCTCAGCGGAAACCTTGAGACATTTTCTCAGGTCTTGATGGAGCAGCAGAGGGAAAGATCCTTGAGAGAGCAAG
AGAGACTGCGCCTCTATTCTTCTGATCCATTTGATCTGGATGCTCAAGCCAGAATAGAAGAAGAGATTCGGCAGCAGAAC
ATCGAAGAAAACATGAACATAGCCATGGAAGAGGCCCCCGAGAGTTTTGGACAAGTGGCAATGCTCTATGTCAACTGCAA
AGTGAATGGATATCCTCTGAAGGCTTTTGTTGACTCAGGAGCCCAAATGACCATCATGAGTCAAGCTTGTGCTGAGAGAT
GTAACATAATTAGGCTGGTGGACCGACGATGGGCTGGAGTTGCTAAGGGAGTGGGCACACAAAGGATTATTGGCCGCATT
CATCTATCTCAGATTCAGATTGAAGGTGACTTCTTACAGTGCTCTTTTTCCATCCTCGAGGAGCAGCCCATGGACGTACT
TCTAGGACTAGATATGCTCAGGAGACATCAGTGTTCCATTGATTTGAAGAAAAATGTGCTGGTGATTGGAACCACTGGCA
CACAGACTCACTTCCTTCCCGAGGGAGAGTTACCCCCCTGTGCTAGGCTGGTAAGTGGAACTGGGCAAGAGGAGTCTTCA
AATAAAGAAGCATCAGATAAAACGAAACGTTCAGTCATGGATTCAGGACGCAAAAAGCATTGA

Alignment

ORF - retro_itri_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.55 %
• Parental protein coverage: 78.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRLPQGAQQPHS-SPGETTSSPQGLDNPALLRDMLLANPHELSLLKERNPPLAEALLSGDLDKFSRVLVE
          Q......QQ.H....GE...S.QGLD.P.L.R.MLL..PH.LSLLKERNP.LAEALLSG.L..FS.VL.E
Retrocopy QKRASSVQQSHGLASGEKMTSSQGLDSPTLIRSMLLSSPHDLSLLKERNPTLAEALLSGNLETFSQVLME

Parental  QQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQQNIEENMTIAMEEAPESFGQVVMLYINCKVNGHPV
          QQ..R..REQER.RL.S.DPFDL.AQA.IEE.IRQQNIEENM.IAMEEAPESFGQV.MLY.NCKVNG.P.
Retrocopy QQRERSLREQERLRLYSSDPFDLDAQARIEEEIRQQNIEENMNIAMEEAPESFGQVAMLYVNCKVNGYPL

Parental  KAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGIAKGVGTQKIIGRVHLAQVQIEGDFLACSFSILEEQP
          KAFVDSGAQMTIMSQACAERCNI.RLVDRRWAG.AKGVGTQ.IIGR.HL.Q.QIEGDFL.CSFSILEEQP
Retrocopy KAFVDSGAQMTIMSQACAERCNIIRLVDRRWAGVAKGVGTQRIIGRIHLSQIQIEGDFLQCSFSILEEQP

Parental  MDMLLGLDMLKRHQCSIDLKKNVLVIGTTGSQTTFLPEGELPECARLAYGAGREDVRPEEIADQ
          MD.LLGLDML.RHQCSIDLKKNVLVIGTTG.QT.FLPEGELP.CARL..G.G.E.....E..D.
Retrocopy MDVLLGLDMLRRHQCSIDLKKNVLVIGTTGTQTHFLPEGELPPCARLVSGTGQEESSNKEASDK

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_93 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_93 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 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011873	1 retrocopy	retro_amel_10,
Bos taurus	ENSBTAG00000018718	2 retrocopies	retro_btau_15, retro_btau_650,
Canis familiaris	ENSCAFG00000016220	1 retrocopy	retro_cfam_193,
Callithrix jacchus	ENSCJAG00000008625	1 retrocopy	retro_cjac_196,
Cavia porcellus	ENSCPOG00000020885	1 retrocopy	retro_cpor_88,
Equus caballus	ENSECAG00000000762	1 retrocopy	retro_ecab_110,
Homo sapiens	ENSG00000197312	1 retrocopy	retro_hsap_96,
Gorilla gorilla	ENSGGOG00000013537	1 retrocopy	retro_ggor_143,
Macropus eugenii	ENSMEUG00000006148	1 retrocopy	retro_meug_1364,
Myotis lucifugus	ENSMLUG00000030669	1 retrocopy	retro_mluc_68,
Macaca mulatta	ENSMMUG00000019912	1 retrocopy	retro_mmul_231,
Monodelphis domestica	ENSMODG00000003515	1 retrocopy	retro_mdom_282,
Mustela putorius furo	ENSMPUG00000016332	1 retrocopy	retro_mputfur_1509,
Mus musculus	ENSMUSG00000078515	1 retrocopy	retro_mmus_67,
Oryctolagus cuniculus	ENSOCUG00000023891	1 retrocopy	retro_ocun_249,
Otolemur garnettii	ENSOGAG00000027709	1 retrocopy	retro_ogar_4,
Ochotona princeps	ENSOPRG00000018448	1 retrocopy	retro_opri_4,
Pongo abelii	ENSPPYG00000001841	1 retrocopy	retro_pabe_158,
Pan troglodytes	ENSPTRG00000024059	1 retrocopy	retro_ptro_570,
Pteropus vampyrus	ENSPVAG00000005084	1 retrocopy	retro_pvam_420,
Rattus norvegicus	ENSRNOG00000012274	1 retrocopy	retro_rnor_2606,
Sus scrofa	ENSSSCG00000003462	1 retrocopy	retro_sscr_6,
Ictidomys tridecemlineatus	ENSSTOG00000019447	1 retrocopy	retro_itri_93 ,
Tarsius syrichta	ENSTSYG00000002522	1 retrocopy	retro_tsyr_1120,