RetrogeneDB ID: retro_onil_5

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831155.1:1364637..1365525(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000021341
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: cdk5r2a
• Ensembl ID: ENSONIG00000009117
• Aliases: None
• Description: cyclin-dependent kinase 5, regulatory subunit 2a (p39) [Source:ZFIN;Acc:ZDB-GENE-050417-22]

Sequence

>retro_onil_5
ATGGGAACCGTTCTCTCTATATCTCCCGCGACCAAGAAGGCGTCGATCATGGATGCCGAGGTCGCAGGAGACGGAGGGAA
AAACGACAAGAGCCTCAAGCGCCACTCCATGTTCGTGTCTCTGTCCTGGAAGAAGCTGGTGGCTAGTTCGGCCAAGAAGA
GCGCAAAGAAAGTGACCCCGAACCCGCTGCCCACTCGAGAGCTGCCGTCCAGCCAGGTGGCTCAGCTCAACAGCGAAAAC
GTGAGGAAAACGCACCAGACCGAAGAGAAGAAACCGAAAGCGCCCATCCCCGTCCCGGTGCCCACGGTCCCCACGCAGAA
CAGCGAGTCTGTCGTGCAGAACGGGAGGCTCTCCTCGGTCCAGAAGCAGCCCAGCAGCGTGTCTCTGGTGTCACCCAGGC
GGATAGTCATCCAGGCTTCAACCGGCGAGCTGCTTCGCTGTTTGGGGGACTTCTTGTGCCGCAGGTGTTACAAACTGAAA
GAGTTAAACAGCGGAGAGGTGATCCTCTGGTTCCGAAACATTGACCGGACTCTTTTGCTCCAGGGCTGGCAGGACCAAGG
CTTCATCACGCCGGCCAACGTGGTGTTCGTGTACCTGCTGTGCGAAGACACGATATCGGACAGCACCGACAGCCCAGCCG
AGCTGCAGGGCACCTTTCAGACTTGCCTCTACCTCGCCTACTCGTACATGGGCAACGAGATTTCCTACCCGCTCAAGCCG
TTCATGAACGAGACGAACAAGGACGTTTTCTGGGAGACATCGCTCCGGATCATCAACAGGATGAGTGCCAAAATGCTTCA
GCTGAATGCAGACCCACACTTTTTCACCGAGGTTTTCCAGGATCTCAAAAACCAGCGCGACAGCAGCGAGTCGAACCTGG
ACCGCTGA

Alignment

ORF - retro_onil_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.74 %
• Parental protein coverage: 59.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRQAQPEPLVSPRRVVVQASTGELLHCLSDFMCQRCIKLKELSSNQIVLWFRNVDRALLVQGWQDQCFIS
          Q.Q.....LVSPRR.V.QASTGELL.CL.DF.C.RC.KLKEL.S....LWFRN.DR.LL.QGWQDQ.FI.
Retrocopy QKQPSSVSLVSPRRIVIQASTGELLRCLGDFLCRRCYKLKELNSGEVILWFRNIDRTLLLQGWQDQGFIT

Parental  PASLVFVYLLCRDVVDEDTASEHELHATFLTCLYLAYSYLGNEISYPLKPFLVESSRDAFWDRALELIER
          PA..VFVYLLC.D.....T.S..EL..TF.TCLYLAYSY.GNEISYPLKPF..E...D.FW...L..I.R
Retrocopy PANVVFVYLLCEDTISDSTDSPAELQGTFQTCLYLAYSYMGNEISYPLKPFMNETNKDVFWETSLRIINR

Parental  LSGDMLRINADPHFFTEVFQDLKKQGASTLDNL
          .S..ML..NADPHFFTEVFQDLK.Q..S...NL
Retrocopy MSAKMLQLNADPHFFTEVFQDLKNQRDSSESNL

Legend:

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

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_5 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_5 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000009117	1 retrocopy	retro_onil_5 ,