RetrogeneDB ID: retro_ttru_744

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3247:123738..124530(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSTTRG00000001793
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_ttru_744
CTCTTCCGCCGCCATTTTAAATCCAGCTCCATACAACGTTCTGTCGCCGCTGCTGCCGCGACACAGATTGCACGCCAGCG
CCTCCCAGCCGATAACTCAGCCGCTATGGAAGACATGAACGAGTACAGCAACATAGAGGAATTTGCAGAGGGATCTAAGA
TCAACGCGAGCAAGAATCAGCAGGATGATGGTAAAATGTTTATTGGAGGCTTGAGCTGGAATACAAACAAGAAAGATCTG
ACTGAATATTTGTCTCAATTTGGGGAAGTTGTAGACTGCACAATTAAAACAGATCCAGTCACTGGAAGATCAAGAGGATT
TGGATTTGTGCTTTTCAAAGATGCTGCTAGTGTTGATAAGGTTTTGGAAATGAAAGAACACAAGCTGGATGGCAAATTGA
TAGACCCTAAAAGAGCCAAAGCTTTAAAAGGGAAGGAACCCCCTAAAAAGGTTTTTGTGGGTGGATTGAGCCCAGATACT
TCAGAAGAACAAATTAAAGAATATTTTGGAGCCTTTGGAGAGATTGAAAATATTGAACTTCCCATGGATACAAAAACAAA
TGAAAGAAGAGGATTTTGTTTTATTACATATACAGACGAAGAGCCAGTAAAGAAATTGTTAGAAAGCAGATACCATCAAA
TTGGTTCTGGGAAGTGTGAAATCAAAGTTGCACAACCCAAAGAGGTATATAGGCAGCAACAGCAACAACAAAAAGGAGGA
AGAGGTGCTGCAGCTGGTGGACGAGGTGGTACTAGGGGTCGTGGCCGAGGCCAACAGAGCACTTATGGCAAG

Alignment

ORF - retro_ttru_744 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 62.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFRRHFKSSSIQRSAAAAAATRIARQRFPADNSAAMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG
          LFRRHFKSSSIQRS.AAAAAT.IARQR.PADNSAAMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG
Retrocopy LFRRHFKSSSIQRSVAAAAATQIARQRLPADNSAAMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG

Parental  LSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEMKEHKLDGKLIDPKRAK
          LSW.T.KKDLTEYLS.FGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEMKEHKLDGKLIDPKRAK
Retrocopy LSWNTNKKDLTEYLSQFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEMKEHKLDGKLIDPKRAK

Parental  ALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESR
          ALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESR
Retrocopy ALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESR

Parental  YHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQ
          YHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQ......
Retrocopy YHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQQSTYGK

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_744 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_744 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 12 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971, retro_meug_2165, retro_meug_249, retro_meug_766,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tursiops truncatus	ENSTTRG00000000709	3 retrocopies	retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744 ,
Tursiops truncatus	ENSTTRG00000004505	27 retrocopies	retro_ttru_1202, retro_ttru_1223, retro_ttru_1251, retro_ttru_1331, retro_ttru_1362, retro_ttru_156, retro_ttru_157, retro_ttru_1678, retro_ttru_1732, retro_ttru_1806, retro_ttru_1813, retro_ttru_1874, retro_ttru_221, retro_ttru_311, retro_ttru_479, retro_ttru_599, retro_ttru_605, retro_ttru_607, retro_ttru_620, retro_ttru_63, retro_ttru_678, retro_ttru_708, retro_ttru_812, retro_ttru_882, retro_ttru_902, retro_ttru_926, retro_ttru_981,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,