RetrogeneDB ID: retro_ttru_1398

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112318:34014..35804(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000004757
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SMEK1
• Ensembl ID: ENSTTRG00000013598
• Aliases: None
• Description: SMEK homolog 1, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:20219]

Sequence

>retro_ttru_1398
ATGACCGACACCCAGCGGCGGGTGAAGGTTTACACACTCAACGAGGACCGGCAGTGGGACGACCGGGGCACCGGGCATGT
GTCGTCAGGCTACGTGGAGCAGCTGAAGGGCATGTCCCTGCTTGTCAGGGCCGAGAGCGACGGTTCTCTACTTTTAGAGT
CCAAAATAAATCCTAATACTGTATACCAGAAACAACAGGACACTTTGATTGTGTGGTCTGAAGCAGAAAATTATGACTTG
GCCCTTAGCTTTCAAGAAAAAGCTGGATGTGATGAAATTTGGGAGAAAATATGTCAGGTTCAAGGAAAGAACCCATCAGT
GGACATCACTCAGGACCTTGTAGATGAGTCTGAAGAGGAGCGTTTCGATGATATGTCATCGGCAGGTTTAGAATTGCCAT
CTTGTGAATTAAGTCGCCTTGAGGAAATTGCAGAACTTGTGGCATCATCTTTACCTTCCCCCCTGCGTCGTGAAAAACTT
GCACTAGCACTGGGAAATGAGGATTACATTAAAAAGCTCTTAGAGCTTTTTCATGTGTGTGAGGATTTGGAAAATATTGA
AGGACTGCACCACTTGTATGAAATTATCAAAGGCATCTTCCTCTTGAATCGAACTGCTCTTTTTGAAGTTATGTTCTCTG
AGGAATGTATAATGGACGTCATTGGATGCTTAGAATATGATCCTGCTTTATCACAACCACGAAAACATAGGGAATTTCTA
TCTAAAACAGCCAAGTTTAAAGAAGTGATTCCCATATCAGATCCTGAGCTGAAACAAAAAATTCATCAGACATACAGAGT
TCAGTATATACAAGGCATGGTTCTACCTACTCCTTCAGTCTTTGAAGAAAATATGTTATCAACACTTCACTATTTTATCT
TTTTCAATAAGGTAAAAATTGTTGGTATGTTACAGGAAGATGAAAAATTTCTGACAGATTTGTTTGCACAGCTAACAGAT
GAAGCAACAGATGAGGAAAAAAGACAGGAATTGGTTAACTTTTTAAAAGAATTTTGTGCATTCTCCCAAACGCTACAACC
TCAAAACAGAGATGCTTTTTTCAAGACTTTGTCAAACATGGGTATATTACCAGCTTTAGAAGTCATCCTTGGCATGGATG
ATACACAGGTGCGAAGTGCTGCTACTGATATATTATCATACTTGGTTAATATAATCCATCCATGGTACGAGAGTTTCTCA
TGCAGGAGGCACAACAGAATGATGATGATATTTTGCTCATCAACCTCATTATAGAACATATGATTTGTGATACAGACCCT
GAACATGGAGGAGCAGTCCAGCTTATGGGCCTCCTTCGAACATTAGTTGACCCAAAAAACATGTTAGCTACTGCCAATAA
AACAGAAAAGACTGAATTTCTGGGTTTCTTCTACAAGCACTGTATGCATGTCCTTACTGCTCCCTTACTGGCAAATACAA
CAGAAGACAAACCTAGCAAAGATGATTTTCAGACTGCCCAGTTGTTGGCACTTGTATTGGAATTGTTAACATTTTGTGTG
GAGCACCATACCTACCACATAAAGAACTACATTATTAATAAGGACATTCTCCGGAGAGTGTTAGTTCTTATGGCCTCGAA
GCATGCTTTCTTGGCATTATGTGCTCTTCGTTTTAAGAGAAAGATTATTGGATTAAAAGATGAGTTTTACAACCACTATA
TAATGAAAAGTTTTTTGTTTGAACCAGTAGTCAAAGCATTTCTCAACAATGGATCCCGCTACAATCTGATGAACTCTGCC
ATAATAGAAATGTTTGAATTTATTAGAGTG

Alignment

ORF - retro_ttru_1398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.82 %
• Parental protein coverage: 72.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDTRRRVKVYTLNEDRQWDDRGTGHVSSGYVERLKGMSLLVSAESDGSLLLESKINPNTAYQKQQDTLI
          MTDT.RRVKVYTLNEDRQWDDRGTGHVSSGYVE.LKGMSLLV.AESDGSLLLESKINPNT.YQKQQDTLI
Retrocopy MTDTQRRVKVYTLNEDRQWDDRGTGHVSSGYVEQLKGMSLLVRAESDGSLLLESKINPNTVYQKQQDTLI

Parental  VWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVDITQDLVDESEEERFDDMSSPGLELPSCELSRL
          VWSEAENYDLALSFQEKAGCDEIWEKICQVQGK.PSVDITQDLVDESEEERFDDMSS.GLELPSCELSRL
Retrocopy VWSEAENYDLALSFQEKAGCDEIWEKICQVQGKNPSVDITQDLVDESEEERFDDMSSAGLELPSCELSRL

Parental  EEIAELVASSLPSPLRREKLALALENEGYIKKLLELFHVCEDLENIEGLHHLYEIIKGIFLLNRTALFEV
          EEIAELVASSLPSPLRREKLALAL.NE.YIKKLLELFHVCEDLENIEGLHHLYEIIKGIFLLNRTALFEV
Retrocopy EEIAELVASSLPSPLRREKLALALGNEDYIKKLLELFHVCEDLENIEGLHHLYEIIKGIFLLNRTALFEV

Parental  MFSEECIMDVIGCLEYDPALSQPRKHREFLTKTAKFKEVIPISDPELKQKIHQTYRVQYIQDMVLPTPSV
          MFSEECIMDVIGCLEYDPALSQPRKHREFL.KTAKFKEVIPISDPELKQKIHQTYRVQYIQ.MVLPTPSV
Retrocopy MFSEECIMDVIGCLEYDPALSQPRKHREFLSKTAKFKEVIPISDPELKQKIHQTYRVQYIQGMVLPTPSV

Parental  FEENMLSTLHSFIFFNKVEIVGMLQEDEKFLTDLFAQLTDEATDEEKRQELVNFLKEFCAFSQTLQPQNR
          FEENMLSTLH.FIFFNKV.IVGMLQEDEKFLTDLFAQLTDEATDEEKRQELVNFLKEFCAFSQTLQPQNR
Retrocopy FEENMLSTLHYFIFFNKVKIVGMLQEDEKFLTDLFAQLTDEATDEEKRQELVNFLKEFCAFSQTLQPQNR

Parental  DAFFKTLSNMGILPALEVILGMDDTQVRSAATDIFSYLVE-YNPSMVREFVMQEAQQNDDDILLINLIIE
          DAFFKTLSNMGILPALEVILGMDDTQVRSAATDI.SYLV..YNPSMVREF.MQEAQQNDDDILLINLIIE
Retrocopy DAFFKTLSNMGILPALEVILGMDDTQVRSAATDILSYLVN<YNPSMVREFLMQEAQQNDDDILLINLIIE

Parental  HMICDTDPELGGAVQLMGLLRTLVDPENMLATANKTEKTEFLGFFYKHCMHVLTAPLLANTTEDKPSKDD
          HMICDTDPE.GGAVQLMGLLRTLVDP.NMLATANKTEKTEFLGFFYKHCMHVLTAPLLANTTEDKPSKDD
Retrocopy HMICDTDPEHGGAVQLMGLLRTLVDPKNMLATANKTEKTEFLGFFYKHCMHVLTAPLLANTTEDKPSKDD

Parental  FQTAQLLALVLELLTFCVEHHTYHIKNYIINKDILRRVLVLMASKHAFLALCALRFKRKIIGLKDEFYNR
          FQTAQLLALVLELLTFCVEHHTYHIKNYIINKDILRRVLVLMASKHAFLALCALRFKRKIIGLKDEFYN.
Retrocopy FQTAQLLALVLELLTFCVEHHTYHIKNYIINKDILRRVLVLMASKHAFLALCALRFKRKIIGLKDEFYNH

Parental  YIMKSFLFEPVVKAFLNNGSRYNLMNSAIIEMFEFIRV
          YIMKSFLFEPVVKAFLNNGSRYNLMNSAIIEMFEFIRV
Retrocopy YIMKSFLFEPVVKAFLNNGSRYNLMNSAIIEMFEFIRV

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_1398 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1398 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000012467	1 retrocopy	retro_dord_714,
Erinaceus europaeus	ENSEEUG00000006324	1 retrocopy	retro_eeur_316,
Pan troglodytes	ENSPTRG00000006638	1 retrocopy	retro_ptro_124,
Pteropus vampyrus	ENSPVAG00000015294	1 retrocopy	retro_pvam_1091,
Tupaia belangeri	ENSTBEG00000008535	1 retrocopy	retro_tbel_2368,
Tarsius syrichta	ENSTSYG00000010333	1 retrocopy	retro_tsyr_863,
Tursiops truncatus	ENSTTRG00000000027	1 retrocopy	retro_ttru_1397,
Tursiops truncatus	ENSTTRG00000013598	1 retrocopy	retro_ttru_1398 ,
Vicugna pacos	ENSVPAG00000002765	1 retrocopy	retro_vpac_536,