RetrogeneDB ID: retro_ttru_1638

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_82176:7841..9253(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000012474
• Aliases: None
• Description: None

Sequence

>retro_ttru_1638
ATGGCGGGGGGCGAGGCTGGTGTGACTCTGGGGCAGCAACATCTTTCTCACCAAGATCTCACCACACTGGATGTTACCAG
GTTGACTCAACTCTCGCATGAAGTTATCAGCAGACAAGCCACAATTAATATAGGTACACTTGGTCACATTGCCCATGGAA
AATCTACCTTTGTGAAAGCTATTTCTGGAATTCACACTGTCAGGTTCAAAAACGAACTAGAAAGAAATATTATGATCAAG
CTTGGATAGGCTAATGTCAAGATTTACAAACTTAATGAGGCAAACTGTCTTAGCCAGAATGTTACAGATCTTATGGAAGT
AGTATACCTGATGAGTTTCCTATAGACATTCCATGGACCAAAGGGAACTTCAGACTAGTCAGACATGTTTTCTTTGTTGA
CTGTCCTGGCCATGATATTTTGATGGCTACTGTGCTGAATGGTGCAGCAGTGATGGTTGCAGCTCTTCGGTTAATAGCTG
GTAATGAATCCTGTCCTCAACCTCAGACTTCTGAACACCTGGCTGCCATAGAAATTATGAAGCTGAAACATATTTTGATT
CTGCAGAATGAAATTGATTTGGTAAAAGAAAGTCAGGCTAAAGAACAGTATGAACAGATCCTTGCATTTGTACAAGGTAC
AGTAGCAAGAGGAGCTCCTATTATTCCAATTTCTGCTCATCTGAAATATAATACTGAAGTTGTCTGTGAGTATATCATTA
AGAAAATTCCAGTACCTCTAAGAGACTTTACTTCAGAACCCCAACTTACTGTTATTAGGTCCTTTGATGTCACCAAACCT
GGCTGTGAGTTTGATGACCTTAAAGGTGGTGTGGCTAGTAGTAGTATTTTAAAAGGAGTATTAAAGGTGGGCCAGGAGAT
AGAAGTCAGACCTGGTATTGTTTCCAAAGATAGCAAAGGAAAACTCGTGTAAACCAATCTTTTCCAAAATTGTATTACTT
TTGAGGAACAAAATGATCTTCAGTATGCTGCTCCAGGGGGTCTTATTGGAGTTGGAAGAAAAATTCACCCCACTTTGTGC
TGGGCTGACAGAATGGTGGGGCACGTACTTGGTGTAGTTGGAGCTTTACCAGAGATCTTCACAGAATTGGAAATTTCCTA
TTTCCTACTTAGACGACTTCTTGGTGTACACATGGAAGGAGACAAAAAAGCAGCAAAGGGTCAAAAGCTATCTAAGAATG
AAGTGCTTATGGTGAACACAGGATCCCTTTCAACAGGAGGAAGAGTTGGGGCAGTCAAGGCTGATTTGGGTAAAATCGTT
CTCACCAATCCTGTGTGCACAGAAGTGGGAGAAAAAATAGCCCTTAGCCAGAGAGTTGAGAAACACTGGTGTTTAATTGG
TTGGGGTCAGATAAGAAGAGGAGTAACAATCAAGCCACCAGCAGATGATGAC

Alignment

ORF - retro_ttru_1638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGGEAGVTLGQPHLSRQDLNTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFK
          MAGGEAGVTLGQ.HLS.QDL.TLDVT.LT.LSHEVISRQATINIGT.GH.AHGKST.VKAISG.HTVRFK
Retrocopy MAGGEAGVTLGQQHLSHQDLTTLDVTRLTQLSHEVISRQATINIGTLGHIAHGKSTFVKAISGIHTVRFK

Parental  NELERNITIKLGYANAKIYKLDDPSCPR-PECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHD
          NELERNI.IKLG.AN.KIYKL....C...PECYRS.GSS.PDEFP.DIP.TKGNF.LVRHV.FVDCPGHD
Retrocopy NELERNIMIKLG*ANVKIYKLNEANCLS<PECYRSYGSSIPDEFPIDIPWTKGNFRLVRHVFFVDCPGHD

Parental  ILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILA
          ILMAT.LNGAAVM.AAL.LIAGNESCPQPQTSEHLAAIEIMKLKHILILQN.IDLVKESQAKEQYEQILA
Retrocopy ILMATVLNGAAVMVAALRLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNEIDLVKESQAKEQYEQILA

Parental  FVQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVA
          FVQGTVA.GAPIIPISA.LKYN.EVVCEYI.KKIPVP.RDFTSEP.L.VIRSFDV.KPGCE.DDLKGGVA
Retrocopy FVQGTVARGAPIIPISAHLKYNTEVVCEYIIKKIPVPLRDFTSEPQLTVIRSFDVTKPGCEFDDLKGGVA

Parental  GGSILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCR
          ..SILKGVLKVGQEIEVRPGIVSKDS.GKL.....F......F.E.NDLQYAAPGGLIGVG.KI.PTLC.
Retrocopy SSSILKGVLKVGQEIEVRPGIVSKDSKGKLV*TNLFQNCIT-FEEQNDLQYAAPGGLIGVGRKIHPTLCW

Parental  ADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSA
          ADRMVG.VLG.VGALPEIFTELEISYFLLRRLLGV..EGDKKAAK.QKLSKNEVLMVN.GSLSTGGRV.A
Retrocopy ADRMVGHVLGVVGALPEIFTELEISYFLLRRLLGVHMEGDKKAAKGQKLSKNEVLMVNTGSLSTGGRVGA

Parental  VKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD
          VKADLGKIVLTNPVCTEVGEKIALS.RVEKHW.LIGWGQIRRGVTIKP..DDD
Retrocopy VKADLGKIVLTNPVCTEVGEKIALSQRVEKHWCLIGWGQIRRGVTIKPPADDD

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_1638 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1638 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638 , retro_ttru_617, retro_ttru_686,