RetrogeneDB ID: retro_itri_326

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:25966385..25966836(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN2
• Ensembl ID: ENSSTOG00000028367
• Aliases: None
• Description: calponin 2 [Source:HGNC Symbol;Acc:2156]

Sequence

>retro_itri_326
TCTAATTTCATCAAGACTGTGTTCGGCATGAACCTTGTTTACCTGTTTGAGGCCAGTGATCTACTTGAGAGTGAGAACAT
GATGCACTTACAGGTGTCTCTTCTTGAGCTGTCAGGGAAAACCAAGACAGAGGGGTTACAGAGGAGGCATGGACATTGGT
GTCAAGTTCTCAGAGAAGCAGGAGTGGAACTTCAATGATGTCATCACAAAGGCTGGTTAGTGTCATAGGGCTGCAGATGA
GTCAACCCAACAAGTGGGTCAACCAGTTGGGCATGATGGCATATGGTACAGGAGGCATCTCTACAACCCAAAAAAGTGTA
TCCTGCCACCCACAGACCACTCCACCATCATCTCCACCATCAGATGAACACAAAAATGTGCTAGCCAGGTAGGTATGATG
ACTTTAGGGACCAAGAAGCTCATCTACCACAAGTGTGGCAACTCCTCATGT

Alignment

ORF - retro_itri_326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.13 %
• Parental protein coverage: 50.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TNFIKAMVSYGMNPVDLFEANDLFESGNITQVQVALLALAGKAKTKGLQ-SSVDIGVKYSERQQRNFDDA
          .NFIK.....GMN.V.LFEA.DL.ES.N....QV.LL.L.GK.KT.GLQ....DIGVK.SE.Q..NF.D.
Retrocopy SNFIKTV--FGMNLVYLFEASDLLESENMMHLQVSLLELSGKTKTEGLQ>GGMDIGVKFSEKQEWNFNDV

Parental  TMKAGQCVIGLQMGT-NKCASQSGMTAYGT-RRHLCDPKNHILPPMDHST-ISLQMGTNKCASQVGMTAP
          ..KAG.C.......T.NK...Q.GM.AYGT.RRHL..PK..ILPP.DHST.IS....T.KCASQVGM...
Retrocopy ITKAG*CHRAADEST>NKWVNQLGMMAYGT<RRHLYNPKKCILPPTDHSTIISTIR*TQKCASQVGMMTL

Parental  GTRRHIYDTKLGTHRC
          GT...IY..K.G...C
Retrocopy GTKKLIYH-KCGNSSC

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_326 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_326 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 8 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000001141	1 retrocopy	retro_dord_672,
Erinaceus europaeus	ENSEEUG00000015171	1 retrocopy	retro_eeur_581,
Gorilla gorilla	ENSGGOG00000028153	9 retrocopies	retro_ggor_1199, retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Nomascus leucogenys	ENSNLEG00000001161	2 retrocopies	retro_nleu_1757, retro_nleu_2893,
Otolemur garnettii	ENSOGAG00000010144	2 retrocopies	retro_ogar_1416, retro_ogar_1733,
Pongo abelii	ENSPPYG00000009302	12 retrocopies	retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,
Ictidomys tridecemlineatus	ENSSTOG00000028367	1 retrocopy	retro_itri_326 ,