RetrogeneDB ID: retro_ttru_44

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_102:115929..117606(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RYK
• Ensembl ID: ENSTTRG00000003760
• Aliases: None
• Description: receptor-like tyrosine kinase [Source:HGNC Symbol;Acc:10481]

Sequence

>retro_ttru_44
CCGCCGGCGCTGCCTACCGCGTACGCGGGGCCTGGCGTGAGCCTCTGCCTGAGAGAGGACGAGGTGCGCCGGCTCATCGG
TTTTGTTGCAGAACTTTATTATGTGAGAAATGATCTTATTAGTCACTACGCCCTATCCTTTAACCCGTTAGTACCCAGCG
AGACAAATTTCGTGCACTTCACTTGGCATGCAAAGTCCAAGGTTGAATATAAGCTGGGATTCCAAGTAGACAATTTCCTG
GCTATGGACGTGCCCCAGGTCAACATTTCTGCTCAGGGGGAAGCTCCACGCACTTTATCAGTGCTTCGGGTCGAGCTTTC
CTGTACTGGCAAAGTAGATTCTGAGGTTATGATACTAATGCAGCTCAACTTGACAGTAAATTCTTCAAAAAACTTTACAG
TCTTAAATTTTAAACGAAGGAAAATGTGCTACAAAAAACTTGAAGAAGTAAAAACGTCATCCTTGGACAAAAACACTAGC
AGAACTATTTATGATCCTGTACATGCGGCTCCAACCACTTCTACGCGTGTGTTTTATATCAGCGTAGGGGTTTGCTGTGC
AGTAATATTTCTCGTAGCAATAATATTAGCTGTTTTGCACCTTCTTCGTATGAAAAGGATTGAACTGGATGACAGCATCA
GTGCCAGCAGTAGTTCCCAAGGGCTGTCTCAGCCATCTAACCAGACGACTCAGTATCTGAGAACCGACACACCCAACAAT
GCAACTCCTATCGCCAGCTCCTCAGGTTATCCCACCTTGCGGATAGAGAAGAATGACCTGAGAAGTGTCACTCTTTTGAA
AGCCAAAGCTAAGGTGAAGGATATCGCAATATCCAGGGAGAGGATAACTCTAAAAGATGTACTCCAAGAAGGTACTTCTG
GGCGTGTTTTCCATGGGATTTTAGTAGATGAAAAAGATCCAAATAAGGAAAAACAAGCATTTGTTAAAAACAGGTAAAGA
TCAAGCTTCTGAAATTCAGGTGACAATGATGCTTACTGAAAGTTGTAAGCTACGAGGTCTTCATCACAGGAATCTTCTTC
CTATTACTCATGTCTGTATAGAAGAAGGAGAAAAGCCCATGGTGATATTGCCTTACATGAATTGGGGGAATCTTAGATTG
TTTTTACGGCAGTGCAGATTAGTAGAGGCCGAAAATCCACAAGCAATTTCTCAACAAGACCTGTCCACGTGGCTATTCAG
ATTGCTTGTGGAATGAGCTATCTGGCCAGAAGGGAAGTCATCCACGAAGACCTGGCTGCTAGGAACTGTGTCATGGATGA
CACACTTCAAGTAAAGATCACAGACAATACCTTCTCCAGAGACTTGTTCCCTATGGACTCTCATTGTCTGGGGGACAACG
AAAACAGGCCAGTTCGGTGGATGGCTCTTGAAAGTCTGGTTAATAATGAGTTCTCCAGTGCTAGTGATGTGTGGGCCTTT
GGAGTGACGCTGTGGGAGCTCATGACTCTGGGCCAAACGCCCTATGTGGACATCGACCCGTTGGAGATGGCCGCGTACCT
GATAGATGGTTACCGAATAGCCCAGCTGATCAACTGTCCTGCTGAACTATTTGCTGTGATGGCTTGTTGCTGGGCCTTAG
GTCCGGAGGAGAGGCCCAAGTTCCAGCAGCTGGTCCAGTGTCTCACAGAGTTCCATGCAGCCCTGGAGGCCTACGTC

Alignment

ORF - retro_ttru_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPALRAASAGPSVSLYMSEDEVRRLIGLDAELYYVRNDLISHYALSFNLLVPSETNFLHFTWHAKSKVEY
          PPAL..A.AGP.VSL...EDEVRRLIG..AELYYVRNDLISHYALSFN.LVPSETNF.HFTWHAKSKVEY
Retrocopy PPALPTAYAGPGVSLCLREDEVRRLIGFVAELYYVRNDLISHYALSFNPLVPSETNFVHFTWHAKSKVEY

Parental  KLGFQVDNFVAMDMPQVNISAQGEVPRTLSVFRVELSCTGKVDSEVMILMQLNLTVNSSKNFTVLNFKRR
          KLGFQVDNF.AMD.PQVNISAQGE.PRTLSV.RVELSCTGKVDSEVMILMQLNLTVNSSKNFTVLNFKRR
Retrocopy KLGFQVDNFLAMDVPQVNISAQGEAPRTLSVLRVELSCTGKVDSEVMILMQLNLTVNSSKNFTVLNFKRR

Parental  KMCYKKLEEVKTSSLDKNTSRTIYDPVHAAPTTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIELD
          KMCYKKLEEVKTSSLDKNTSRTIYDPVHAAPTTSTRVFYISVGVCCAVIFLVAIILAVLHL..MKRIELD
Retrocopy KMCYKKLEEVKTSSLDKNTSRTIYDPVHAAPTTSTRVFYISVGVCCAVIFLVAIILAVLHLLRMKRIELD

Parental  DSISASSSSQGLSQPSTQTTQYLRADTPNNATPITSSSGYPTLRIEKNDLRSVTLLEAKAKVKDIAISRE
          DSISASSSSQGLSQPS.QTTQYLR.DTPNNATPI.SSSGYPTLRIEKNDLRSVTLL.AKAKVKDIAISRE
Retrocopy DSISASSSSQGLSQPSNQTTQYLRTDTPNNATPIASSSGYPTLRIEKNDLRSVTLLKAKAKVKDIAISRE

Parental  RITLKDVLQEGTFGRIFHGILVDEKDPNKEKQAFV-KTVKDQASEIQVTMMLTESCKLRGLHHRNLLPIT
          RITLKDVLQEGT.GR.FHGILVDEKDPNKEKQAFV.KT.KDQASEIQVTMMLTESCKLRGLHHRNLLPIT
Retrocopy RITLKDVLQEGTSGRVFHGILVDEKDPNKEKQAFV>KTGKDQASEIQVTMMLTESCKLRGLHHRNLLPIT

Parental  HVCIEEGEKPMVILPYMNWGNLKLFLRQCKLVEANNPQAISQQDL-VHMAIQIACGMSYLARREVIHKDL
          HVCIEEGEKPMVILPYMNWGNL.LFLRQC.LVEA.NPQAISQQDL.VH.AIQIACGMSYLARREVIH.DL
Retrocopy HVCIEEGEKPMVILPYMNWGNLRLFLRQCRLVEAENPQAISQQDL<VHVAIQIACGMSYLARREVIHEDL

Parental  AARNCVIDDTLQVKITDNALSRDLFPMDYHCLGDNENRPVRWMALESLVNNEFSSASDVWAFGVTLWELM
          AARNCV.DDTLQVKITDN..SRDLFPMD.HCLGDNENRPVRWMALESLVNNEFSSASDVWAFGVTLWELM
Retrocopy AARNCVMDDTLQVKITDNTFSRDLFPMDSHCLGDNENRPVRWMALESLVNNEFSSASDVWAFGVTLWELM

Parental  TLGQTPYVDIDPFEMAAYLKDGYRIAQPINCPDELFAVMACCWALDPEERPKFQQLVQCLTEFHAALGAY
          TLGQTPYVDIDP.EMAAYL.DGYRIAQ.INCP.ELFAVMACCWAL.PEERPKFQQLVQCLTEFHAAL.AY
Retrocopy TLGQTPYVDIDPLEMAAYLIDGYRIAQLINCPAELFAVMACCWALGPEERPKFQQLVQCLTEFHAALEAY

Parental  V
          V
Retrocopy V

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_44 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_44 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016999	2 retrocopies	retro_btau_790, retro_btau_793,
Loxodonta africana	ENSLAFG00000016402	1 retrocopy	retro_lafr_333,
Tursiops truncatus	ENSTTRG00000003760	1 retrocopy	retro_ttru_44 ,