RetrogeneDB ID: retro_ttru_1823

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_92872:147642..148239(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2B
• Ensembl ID: ENSTTRG00000011903
• Aliases: None
• Description: general transcription factor IIB [Source:HGNC Symbol;Acc:4648]

Sequence

>retro_ttru_1823
GCAACAAAAGATCCATCTCGAGGTGGAGATTCTCAGAATCCTCTTCTGAGTGATGGAGATTTGTCTACTATGAATGGCAA
GGGTACAGGAGCTGCAAGTTTGGATGAATGTGGTAATTCTAAGTACCAGAATAGGAGAACCATAAGTAGTTCTGATCGGG
CGATGATGAATGCATTCAAAGAAATCACTACCATGGCAGACAGAATCAACCTCCCTCGAAATATAGTTGGTTGAACAAAT
AATCTATTCAAGCAAGCATATGAACAGAAGAGCCTGAAGGGAAGGGCTAATGATGCCATAGCTTCTGCTTGTCTCTATAT
TGCCTGCAGACAGGAAGGAGTTCCTAGGACATTTAAAGAAATACGTGCTATATCACAAATTTCTAAGAAAGAAATTGGTC
GATGTTTTAAACTTATTTTGAAAGCTTTAGAAACCAGTGTGGATTTGATTACAACTGGGGACTTCATGTCCAGGTTTTGT
TCCAACCTTTGCCTTCCTAAACAAGTACAGATGGCAGCTACACATATAGCCCATAAAGCTGTGGAGTTGGACTTGGTTCC
TGGAAGGAGCCCGATATCTGTGGCAGGAGCCGCCATT

Alignment

ORF - retro_ttru_1823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.47 %
• Parental protein coverage: 62.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATKDPSRVGDSQNPLLSDGDLSTMIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRIN
          ATKDPSR.GDSQNPLLSDGDLSTM.GKGTGAAS.DE.GNSKYQNRRT.SSSDRAMMNAFKEITTMADRIN
Retrocopy ATKDPSRGGDSQNPLLSDGDLSTMNGKGTGAASLDECGNSKYQNRRTISSSDRAMMNAFKEITTMADRIN

Parental  LPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLIL
          LPRNIV..TNNLFKQ.YEQKSLKGRANDAIASACLYIACRQEGVPRTFKEI.A.S.ISKKEIGRCFKLIL
Retrocopy LPRNIVG*TNNLFKQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEIRAISQISKKEIGRCFKLIL

Parental  KALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAI
          KALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIA.KAVELDLVPGRSPISVA.AAI
Retrocopy KALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIAHKAVELDLVPGRSPISVAGAAI

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_1823 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1823 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028271	1 retrocopy	retro_mmus_3165,
Sarcophilus harrisii	ENSSHAG00000005314	1 retrocopy	retro_shar_585,
Tupaia belangeri	ENSTBEG00000001398	2 retrocopies	retro_tbel_1988, retro_tbel_2988,
Tursiops truncatus	ENSTTRG00000011903	1 retrocopy	retro_ttru_1823 ,