RetrogeneDB ID: retro_itri_1284

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393427.1:4175085..4175560(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDRG3
• Ensembl ID: ENSSTOG00000022531
• Aliases: None
• Description: NDRG family member 3 [Source:HGNC Symbol;Acc:14462]

Sequence

>retro_itri_1284
ATTACAGTTGGAACTGGAGCTTACAGCCTTAGCAGATTTGCATTCAGTCATCCAGAGCTTGTGGAAGGACTTGTGCTCAT
TAACATTGACCCTTGTGCTAAAGGTTGGATTGACTGGGCAGCTTCCAAACTCCCAGGCTTGACAACCAATGTTGTGAATA
TTATTTTGGCTCATTACTTTGAATAGGAAGAATTGCAGGCCAACCTGGACCTGATTTATACTTACAGTCTATGTATTGCA
CAAAATATCAACCAAAAAAATCTATGGCTCTTCCTGGGTTCCTACAATAAACTCACAGGCCTAGAGATTGAAAAATCTAT
ACAGGGCCAACATAATATCTGATTGAAAATATGGAAGTGTTCTCTTTACTGATAGTAGGGGAAATTTACCTGCAGTTGAG
GTTATGATTGATTATAATTATTGTCCAAAATCTATAGAAACAACTTAACTACTAATGGTGAACTGTGAAGGACTG

Alignment

ORF - retro_itri_1284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.7 %
• Parental protein coverage: 51.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IGVGAGAYILSRFALNHPELVEGLVLINVDPCAKGWIDWAASKLSGLTTNVVDIILAHHFGQEELQANLD
          I.VG.GAY.LSRFA..HPELVEGLVLIN.DPCAKGWIDWAASKL.GLTTNVV.IILAH.F..EELQANLD
Retrocopy ITVGTGAYSLSRFAFSHPELVEGLVLINIDPCAKGWIDWAASKLPGLTTNVVNIILAHYFE*EELQANLD

Parental  LIQTYRLHIAQDINQENLQLFLGSYNGRRDLEIERPILGQNDNRLKTLKCS-TLLVVGD-NSPAVEAVVE
          LI.TY.L.IAQ.INQ.NL.LFLGSYN....LEIE..I.GQ....LK..KCS..LL.VG..N.PAVE....
Retrocopy LIYTYSLCIAQNINQKNLWLFLGSYNKLTGLEIEKSIQGQHNI*LKIWKCS<SLLIVGE<NLPAVEVMID

Parental  CNSRLNPINTTLLKMADCGGL
          .N.....I.TT.L.M..C.GL
Retrocopy YNYCPKSIETT*LLMVNCEGL

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_1284 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1284 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012562	1 retrocopy	retro_amel_378,
Echinops telfairi	ENSETEG00000002250	1 retrocopy	retro_etel_2102,
Myotis lucifugus	ENSMLUG00000009735	1 retrocopy	retro_mluc_1054,
Otolemur garnettii	ENSOGAG00000000895	1 retrocopy	retro_ogar_515,
Sus scrofa	ENSSSCG00000007322	5 retrocopies	retro_sscr_1116, retro_sscr_144, retro_sscr_519, retro_sscr_539, retro_sscr_937,
Ictidomys tridecemlineatus	ENSSTOG00000022531	1 retrocopy	retro_itri_1284 ,