RetrogeneDB ID: retro_ttru_728

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3184:299806..300325(+)
• Located in intron of: ENSTTRG00000002485

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS4X
• Ensembl ID: ENSTTRG00000006164
• Aliases: None
• Description: ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]

Sequence

>retro_ttru_728
GCTCCTCGTCCATCTACCAGTCCCCACAAGCTGAGGGAATGTCTCCCCCTAATTATTTTCCTAAGGAACAGACTTAAATA
TGCCCTAACAGGAGATGAAGTAAAGAAGATCTGCATGCAGCGTTTCATTAAGATTGATGGCAAGGTCCGCACTGATATAA
CCTACCCTGTTGGTTTTATGGATGTCATCAGCATTGACAAGACTGGAGAGAATTTTCGTCTGATCTATGACACCAAGGGT
CGCTTTGCTGTTCATCGTATTACACCTGAGGAGGCCGAGTATAAGTTATGCAAAGTGAGAAAGATCTTTGTGGGGACAAA
AGGAATCCCTCATCTGGTGACCCATGATGCTCGCACCATCCGCTACCCTGATCCCCTCATCAAGGTGAATGACACCATTC
AGATTGATTTGGAGACTGGCAAGATTACTGATTTCATCAAATTTGACACTGGTAACCTGTGCATGGTGACTGGAGGTGCT
AACCTGGGAAGAATTGGTGTGATCACTAACCGGGAGAGA

Alignment

ORF - retro_ttru_728 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.27 %
• Parental protein coverage: 86.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGE
          APRPST.PHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYP.GFMDVISIDKTGE
Retrocopy APRPSTSPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYPVGFMDVISIDKTGE

Parental  NFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETG
          NFRLIYDTKGRFAVHRITPEEA.YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETG
Retrocopy NFRLIYDTKGRFAVHRITPEEAEYKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETG

Parental  KITDFIKFDTGNLCMVTGGANLGRIGVITNRER
          KITDFIKFDTGNLCMVTGGANLGRIGVITNRER
Retrocopy KITDFIKFDTGNLCMVTGGANLGRIGVITNRER

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_728 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_728 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 13 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Ailuropoda melanoleuca	ENSAMEG00000005805	14 retrocopies	retro_amel_1003, retro_amel_1128, retro_amel_1296, retro_amel_1381, retro_amel_1695, retro_amel_1869, retro_amel_195, retro_amel_259, retro_amel_327, retro_amel_576, retro_amel_767, retro_amel_869, retro_amel_968, retro_amel_971,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Gorilla gorilla	ENSGGOG00000023079	18 retrocopies	retro_ggor_1278, retro_ggor_1319, retro_ggor_1354, retro_ggor_1367, retro_ggor_1478, retro_ggor_1479, retro_ggor_1517, retro_ggor_1520, retro_ggor_1689, retro_ggor_223, retro_ggor_2676, retro_ggor_2719, retro_ggor_572, retro_ggor_711, retro_ggor_844, retro_ggor_894, retro_ggor_895, retro_ggor_939,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Tursiops truncatus	ENSTTRG00000006164	13 retrocopies	retro_ttru_104, retro_ttru_1104, retro_ttru_1129, retro_ttru_1748, retro_ttru_260, retro_ttru_465, retro_ttru_470, retro_ttru_512, retro_ttru_565, retro_ttru_618, retro_ttru_631, retro_ttru_728 , retro_ttru_734,