RetrogeneDB ID: retro_ttru_75

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1135:168138..169768(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK6
• Ensembl ID: ENSTTRG00000016253
• Aliases: None
• Description: mitogen-activated protein kinase 6 [Source:HGNC Symbol;Acc:6879]

Sequence

>retro_ttru_75
ATGGCAGAGAAATTTGAAAGTCTCATGAACATTCATGGTTTTGATCTGGGCTCTAGGTATATGGACTTAAAACCATTGGG
TTGTGGAGGCAATGGCTTGGTTTTTTCTGCTGTAGACAATGACTGTGACAAAAGAGTAGCCGTCAAGAAAATCGTCCTTA
CTGATCCCCAGAGTGTCAAACATGCTCTACGTGAAACCAAAATTATTAGAAGACTTGGCCATGATAACATTGTGAAGGTG
TTTGAAATTCTTGGTCCTAGTGGAAGCCAGTTAACAGATGTTGTGGGGTCTTACCAAGCTGAACAGTGTTTACACCGTTC
AGGAGTACATGGAGACAGACTTGGCTAATGTGCTGGAGCAGGGCCCGTTACTGGAAGAGCTTGCCAGGCTTTTCATGCAT
CAGCTGCTACGTGGGCTCAAATATATTCACTCAGCAAACGTACTGCACAGAGATCTCAAACTAGCTAATCTTTTCATTAA
TACTGAAGACTTGGTGCTGAAGATAGGCGACTTTGGTCTTGCACGGATCATAGATCCCCATTGTTCCCATAAGGGTCGTC
TTTCTGAAGGATTGGTTACTAAATGGTACAGATCTCCACGTCTTTTACTTTCTCCTAATAATTATACTAAAGCCATTGAC
ATGTGGGCTGCAGGCTGCATCTTTGCTGAAATACTGACTGGTAAAACCCTCTTTGCAGGTGCCCATGAACTTGAACAGAT
GCAGCTGATTTTAGAGTCTATTCCTGTTGTACGTGAGGAAGATTGACAGGAGCTTCTCAGCATAATTCCAGTTTACATTA
GAAATGACATGACTGAGCCACACAAACCTTTAACTCAGCTGCTTCCGGGAATTAGTCGAGAAGCACTGGATTTCCTGGGA
CAAATTTTGACATTTAGTCCCGTGGATCGGTTGACAGCAGAAGCAGCGCTGTCCCTTCCTTACATGAGCATTTATTCTTT
TCCAATGGATGAGCCAATTTCAAGTCATCCTTTTCGTATTGAAGATGAAGTTGATGATATTTTGCTTATGGATGAAACTC
ATAGTCACATTTATAACTGGGAAAGGTACCATGATTGTCAATTTTCAGAGCATGATTGGCCTATACATAACAACTGTGAT
ATTGATGAAGTTCAGCTTGACCCAAGAGCTCTGTGCCATGTGACTGATGAAGAAGAAGTACAAGTCGATCCTTGAAAATA
TTTGGATGGAGATTGTGAGAAGTATTTGGAGGATCCTGCTTTTGACACCAGTTACTCTACTGAGCCTTGTTGGCAATACC
CAGATCATCATGAAAACAAGTATTGTGATCTGGAGCGTAGCCATACTTGTGACTACAAAACGAGGTCATCATCACATTTA
GATAACTTAGTCTGGAGAGAGAGGGAAGTTAATCATTACTATGAACCCAAGCTTATTATAGATCTTTCCAATTGGAAAGA
ACAAAGCAAAGAAAAATCTGATAAGAAAGGCAAGTCAAAATGTGAAAGCAATGGATTGGTTAAAGCCCAGATAGCTCTAG
AGGAAGCATCACAGCAACTGGCTGAAAAAGAAAGGGAAAAGAATCAGGGATTTGACTTTGATTCCTTTATTGCAGGAACT
ATTCAACTTAGTTCACAGCATGAGCCTACT

Alignment

ORF - retro_ttru_75 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.58 %
• Parental protein coverage: 75.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIR
          MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVA.KKIVLTDPQSVKHALRE.KIIR
Retrocopy MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAVKKIVLTDPQSVKHALRETKIIR

Parental  RLDHDNIVKVFEILGPSGSQLTDDV-GSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRG
          RL.HDNIVKVFEILGPSGSQLT.DV...LT.LNSVY.VQEYMETDLANVLEQGPLLEE.ARLFM.QLLRG
Retrocopy RLGHDNIVKVFEILGPSGSQLT-DV>WGLTKLNSVYTVQEYMETDLANVLEQGPLLEELARLFMHQLLRG

Parental  LKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNY
          LKYIHSANVLHRDLK.ANLFINTEDLVLKIGDFGLARI.DPH.SHKG.LSEGLVTKWYRSPRLLLSPNNY
Retrocopy LKYIHSANVLHRDLKLANLFINTEDLVLKIGDFGLARIIDPHCSHKGRLSEGLVTKWYRSPRLLLSPNNY

Parental  TKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLT
          TKAIDMWAAGCIFAE.LTGKTLFAGAHELEQMQLILESIPVV.EED.QELLS.IPVYIRNDMTEPHKPLT
Retrocopy TKAIDMWAAGCIFAEILTGKTLFAGAHELEQMQLILESIPVVREED*QELLSIIPVYIRNDMTEPHKPLT

Parental  QLLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHS
          QLLPGISREALDFL.QILTFSP.DRLTAE.ALS.PYMSIYSFPMDEPISSHPF.IEDEVDDILLMDETHS
Retrocopy QLLPGISREALDFLGQILTFSPVDRLTAEAALSLPYMSIYSFPMDEPISSHPFRIEDEVDDILLMDETHS

Parental  HIYNWERYHDCQFSEHDWPIHNNFDIDEVQLDPRALSDVTDEEEVQVDPRKYLDGDREKYLEDPAFDTSY
          HIYNWERYHDCQFSEHDWPIHNN.DIDEVQLDPRAL..VTDEEEVQVDP.KYLDGD.EKYLEDPAFDTSY
Retrocopy HIYNWERYHDCQFSEHDWPIHNNCDIDEVQLDPRALCHVTDEEEVQVDP*KYLDGDCEKYLEDPAFDTSY

Parental  STEPCWQYSDHHENKYCDLECSHTCNYKTRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDK
          STEPCWQY.DHHENKYCDLE.SHTC.YKTRSSS.LDNLVWRE.EVNHYYEPKLIIDLSNWKEQSKEKSDK
Retrocopy STEPCWQYPDHHENKYCDLERSHTCDYKTRSSSHLDNLVWREREVNHYYEPKLIIDLSNWKEQSKEKSDK

Parental  KGKSKCERNGLVKAQIALEEASQQLAEKEREKNQGFDFDSFIAGTIQLSSQHEPT
          KGKSKCE.NGLVKAQIALEEASQQLAEKEREKNQGFDFDSFIAGTIQLSSQHEPT
Retrocopy KGKSKCESNGLVKAQIALEEASQQLAEKEREKNQGFDFDSFIAGTIQLSSQHEPT

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_75 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_75 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000962	1 retrocopy	retro_cjac_2633,
Homo sapiens	ENSG00000069956	2 retrocopies	retro_hsap_1257, retro_hsap_2519,
Gorilla gorilla	ENSGGOG00000004003	1 retrocopy	retro_ggor_1571,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63,
Nomascus leucogenys	ENSNLEG00000006476	2 retrocopies	retro_nleu_1441, retro_nleu_2095,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464, retro_ptro_2743, retro_ptro_3045,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445,
Tupaia belangeri	ENSTBEG00000007876	2 retrocopies	retro_tbel_1879, retro_tbel_2946,
Tursiops truncatus	ENSTTRG00000016253	2 retrocopies	retro_ttru_322, retro_ttru_75 ,