RetrogeneDB ID:

retro_sara_558

Retrocopy
location
Organism:Shrew (Sorex araneus)
Coordinates:scaffold_233623:148704..149232(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IK
Ensembl ID:ENSSARG00000007388
Aliases:None
Description:IK cytokine, down-regulator of HLA II [Source:HGNC Symbol;Acc:5958]


Retrocopy-Parental alignment summary:






>retro_sara_558
CTGAGCTGGTCAGCATCACGGCAAACTACAGGGCCGTGGGCCCCACTGCTGAGGCAGACATCAGCTGCAGAGAAAAGACA
GTTGATCCAGGAGTCCAAGTTCTTGGGTGGTGACATGGAATATACCCATTTGGTGAAAGGCTTGGATTTTGCTCTGCTTC
AGAAGATTCGAGCGGAGATTGCCAGCAAGGAGAAAGAGGAGGAAGAACTGATGGAAAAGCCCCAGAAGGAAACCAAGAAA
GACAAGGACCCTGAAAACAAAATTGAATTTAAAACACGTTTAGGCCGCAATGTTTACCGTATGTTCTTCAAGAGCAAAGC
GTACTAACGGAATGAGCTGTTCCTGTCGGGCCGCATGGCCTATGTGGTGGACCTGGATGATGAGTATGCGGACACGGACA
TCCCCACCACTCTTATCCGAAGCAAGGCGGACTGCCCCACCGTGGAGGCCCAGACCACACTGACAACAAGTGACATTGTC
ATCAGCAAGCTCACACAGATTCTTTCCTACTTGAGGCAGGGTACCCGT

ORF - retro_sara_558 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.66 %
Parental protein coverage: 57.76 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalISTTANYRAVGPTAEA-DKSAAEKRRQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEEL
.S..A.....GP.A.......A...RQLIQESKFLGGDME.THLVKGLDFALLQK.RAEIASKEKEEEEL
RetrocopyLSWSASRQTTGPWAPLLRQTSAAEKRQLIQESKFLGGDMEYTHLVKGLDFALLQKIRAEIASKEKEEEEL
ParentalMEKPQKETKKDEDPENKIEFKTRLGRNVYRMLFKSKAYERNELFLPGRMAYVVDLDDEYADTDIPTTLIR
MEKPQKETKKD.DPENKIEFKTRLGRNVYRM.FKSKAY.RNELFL.GRMAYVVDLDDEYADTDIPTTLIR
RetrocopyMEKPQKETKKDKDPENKIEFKTRLGRNVYRMFFKSKAY*RNELFLSGRMAYVVDLDDEYADTDIPTTLIR
ParentalSKADCPTMEAQTTLTTNDIVISKLTQILSYLRQGTR
SKADCPT.EAQTTLTT.DIVISKLTQILSYLRQGTR
RetrocopySKADCPTVEAQTTLTTSDIVISKLTQILSYLRQGTR

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






Sorex araneus was not studied using RNA-Seq expression data.
Sorex araneus was not studied using ChIP-Seq data.
Sorex araneus was not studied using EST data.
Sorex araneus was not studied using FANTOM5 data.
retro_sara_558 was not experimentally validated.

Retrocopy orthology:
Sorex araneus 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 8 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000097273 retrocopies
Dipodomys ordii ENSDORG000000065844 retrocopies
Homo sapiens ENSG000001131411 retrocopy
Gorilla gorilla ENSGGOG000000133741 retrocopy
Loxodonta africana ENSLAFG000000081521 retrocopy
Otolemur garnettii ENSOGAG000000142811 retrocopy
Pongo abelii ENSPPYG000000158611 retrocopy
Sorex araneus ENSSARG00000007388 3 retrocopies
retro_sara_416, retro_sara_419, retro_sara_558 ,



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