RetrogeneDB ID: retro_dord_672

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_508:28195..28889(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cnn2
• Ensembl ID: ENSDORG00000001141
• Aliases: None
• Description: calponin 2 [Source:MGI Symbol;Acc:MGI:105093]

Sequence

>retro_dord_672
ATGAGCTCCACGCAGTTCAACAAGGGGCCATCGTATGGACTCTAGGCCGAAGTCAAGAACCGGCTCCTGTCCAAATATGA
CCCCCAGAAGGAGGCTGAGCTCCGCAGCTGGATCGAAGGGCTCACGGGCCTCTCCATCGGCCCCGACTTCCAGAAGGGTC
TGAAGGACGGGGTGATCTTGTGTACACTCATGAACAAGCTGCAGCCGGGCTCGGCCTCCAAGATCAACCGCTCCATGCAG
AACTGGCACCAGCTAGAAACCTCTCCAACTTCGTCAGGCCATGGTCAGCTACGGCATGAACCCTGTGGACATGTGTGAGG
CTAACGACTTGTTGGAGAGTGGGAACATGACACAGGTTCAGGTGTCGCTTCTCGCACTGGCAGGAAAGGCTAAGACAAAA
GGGCTGCAGAGGGGCGTGGACATCGGGGTCAAGTACTCGGAGAAGCAGCAGCGGAACTTCGATGATGCCACCATGAAGGC
TGGCCAGTGTGTCATTGGGCTGCAGATGGGCACCCACAAATGTGCCAGCCAGTCTGGTATGACAGCCTATGGCACCAGGC
GGCATCTCTACGACCCCAAGAACCACATCCTGCCCCCCATGGACCACTCCACCATCAGCCTTCAGATGGGCACGAACAAC
TGTGCCAGTCAGGTGGGCAGGACGGCTCCGGGGACCCAGCGACACATCTATGAA

Alignment

ORF - retro_dord_672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 75.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRSWIEGLTGLSIGPDFQKGLKDGVILCTLMNKLQPG
          MSSTQFNKGPSYGL.AEVKNRLLSKYDPQKEAELRSWIEGLTGLSIGPDFQKGLKDGVILCTLMNKLQPG
Retrocopy MSSTQFNKGPSYGL*AEVKNRLLSKYDPQKEAELRSWIEGLTGLSIGPDFQKGLKDGVILCTLMNKLQPG

Parental  SVSKINRSMQNWHQLE-NLSNFIK-AMVNYGMNPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGLQS
          S.SKINRSMQNWHQLE.NLSNF...AMV.YGMNPVD..EANDL.ESGNMTQVQVSLLALAGKAKTKGLQ.
Retrocopy SASKINRSMQNWHQLE<NLSNFVR<AMVSYGMNPVDMCEANDLLESGNMTQVQVSLLALAGKAKTKGLQR

Parental  GVDIGVKYSEKQQRNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISL
          GVDIGVKYSEKQQRNFDDATMKAGQCVIGLQMGT.KCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISL
Retrocopy GVDIGVKYSEKQQRNFDDATMKAGQCVIGLQMGTHKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISL

Parental  QMGTNKCASQVGMTAPGTRRHIYD
          QMGTN.CASQVG.TAPGT.RHIY.
Retrocopy QMGTNNCASQVGRTAPGTQRHIYE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_672 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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,