RetrogeneDB ID: retro_ttru_58

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_108:23860..24179(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FT
• Ensembl ID: ENSTTRG00000010405
• Aliases: None
• Description: Ferritin [Source:UniProtKB/TrEMBL;Acc:B6VQP8]

Sequence

>retro_ttru_58
CTGCAGAACCAAAAAGTGGACACATTTGCCTCAAGATATCAATAAAGCCAGCCCTGATGATGGGAGAGCAGGTTGATCAC
AATGGACTGTGCATAACACCCAGACAATGTGTGAATCTATTATTGCTGGAACTACAAAACTGGCTACAGACAAGAGTGAC
ACCCATTTGTTTGACTTCCTTGAGACTCATTTCAAGCAGATGAAATCCATTTTAAAAATGAATGATTATATAATAAACTT
GTGTAAGACAGGGGTTCAGGAATCTGGCATCACAGTATGTACCTTTGACAAGCACACCCTGGGAGACAGTGACAATAAG

Alignment

ORF - retro_ttru_58 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.04 %
• Parental protein coverage: 60.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LQNQR-GGRIFL-QDIKKPDRDD-WENGLNAMECALHLE-KSVNQSLLELH-KLATEKNDPHLCDFLETH
          LQNQ...G.I.L.QDI.K...DD.WE..L..M.CA.H.....VN..LLEL..KLAT.K.D.HL.DFLETH
Retrocopy LQNQK<SGHICL<QDINKASPDD<WESRLITMDCA*HPD<QCVNLLLLELQ<KLATDKSDTHLFDFLETH

Parental  YLNEQVKSIKELGDHVTNLRTMGAPESGMAQYLFDKHTLGNSDNE
          ....Q.KSI....D...NL...G..ESG.....FDKHTLG.SDN.
Retrocopy F--KQMKSILKMNDYIINLCKTGVQESGITVCTFDKHTLGDSDNK

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_58 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_58 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 4 parental genes, and 93 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008947	8 retrocopies	retro_eeur_236, retro_eeur_268, retro_eeur_313, retro_eeur_348, retro_eeur_376, retro_eeur_384, retro_eeur_391, retro_eeur_483,
Latimeria chalumnae	ENSLACG00000017426	1 retrocopy	retro_lcha_75,
Tursiops truncatus	ENSTTRG00000001252	66 retrocopies	retro_ttru_1000, retro_ttru_1071, retro_ttru_108, retro_ttru_1092, retro_ttru_1121, retro_ttru_1134, retro_ttru_1191, retro_ttru_1197, retro_ttru_1208, retro_ttru_1214, retro_ttru_1230, retro_ttru_1234, retro_ttru_1243, retro_ttru_1258, retro_ttru_1259, retro_ttru_1260, retro_ttru_1280, retro_ttru_1284, retro_ttru_1313, retro_ttru_1327, retro_ttru_1352, retro_ttru_146, retro_ttru_1460, retro_ttru_1461, retro_ttru_1487, retro_ttru_1489, retro_ttru_1517, retro_ttru_1547, retro_ttru_1574, retro_ttru_1590, retro_ttru_1636, retro_ttru_1642, retro_ttru_1657, retro_ttru_1675, retro_ttru_1688, retro_ttru_1728, retro_ttru_1751, retro_ttru_1753, retro_ttru_1761, retro_ttru_1791, retro_ttru_1805, retro_ttru_1842, retro_ttru_1870, retro_ttru_1936, retro_ttru_201, retro_ttru_320, retro_ttru_321, retro_ttru_343, retro_ttru_346, retro_ttru_39, retro_ttru_452, retro_ttru_525, retro_ttru_665, retro_ttru_743, retro_ttru_753, retro_ttru_759, retro_ttru_797, retro_ttru_811, retro_ttru_823, retro_ttru_835, retro_ttru_847, retro_ttru_877, retro_ttru_895, retro_ttru_939, retro_ttru_943, retro_ttru_960,
Tursiops truncatus	ENSTTRG00000010405	18 retrocopies	retro_ttru_1059, retro_ttru_1107, retro_ttru_112, retro_ttru_121, retro_ttru_1395, retro_ttru_1484, retro_ttru_152, retro_ttru_1568, retro_ttru_1680, retro_ttru_1760, retro_ttru_1765, retro_ttru_1829, retro_ttru_1881, retro_ttru_248, retro_ttru_517, retro_ttru_58 , retro_ttru_834, retro_ttru_97,