RetrogeneDB ID: retro_tsyr_1444

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_44343:13716..14969(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT1
• Ensembl ID: ENSTSYG00000014610
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1) [Source:HGNC Symbol;Acc:4123]

Sequence

>retro_tsyr_1444
ATGAGAAAATTTGCTTATTGCAAGGTGGTCCTAGCCACCTCCTTGATTTGGGTACTCTTGGATATGTTTCTGCTGCTTTA
CTTTAGTGAATGCAACAAATGTGATGAAAAAAGGAAAGAGGACTACCTGCTGGGGATGTTTTAGAGCCAGTACAAAAGCT
TCACTTAGGTCCTGGAGAAATGGGGAAGCCAGTCGTCATTCCTAAAGAGGATCAAGACAAGATGAAAGAGATGTTTAAAA
TCAATCAGTTCAACTTAATGGTAAGTGAGATGACTGCACTCAACAGATCCTTACAAGATGTAAGGTTAGAAGGGTATAAA
ACAAAGGTGCATCCAGATAATCTTCCTACAACAAGTGTGGTGATTGTTTTCCACTATGAGGCTTGGAGCACACTTCTGCG
AAATGTCCATAGTGTCATTAATCGCTCACCAAGATACATGATAGAAGAAATTGTTCTAGTAGATGATGCCAGTGAAAGAG
ACTTTTTGAAAAGACCTCTAGAGAGTTACGTGAAAAAACTAAAAGTACCAGTTCATGTCATTCAAATGGAGCAGTGTTCT
GGATTGATCAGAGCTAGATTAAAGGGAGTTGCTGTGTCTAAAGGCCAAGTGATCACCTTCCTGGATGCTCACTGTGAGTG
CACAGTGGGATGGCTGGAGCCTCACTTAGCCAGGATCAAACAGGACAGGAGAACAGTGGTATGTCCTATCATCGACGTGA
TCAGCAACGATACTTTCGAGTACATGGCAGGCTCCGATATGACCTATGGTGGGTTCAACTGGAAGCCAAATTTTCACTGG
TATCCTGTTCCCCAAAGAGAAATGGACAGAAGGAAAGGTGATTGGATTCTTCCTATCAGAACACCTACAATGGCAGGAGG
CCTTTTTTCAATAGACAGAGGTTACTTTCAGGAAATTGGAACATATGATGCTGGAATGGATATTTGGGGAGGAGAAAACC
TAGAAATTTCCTTTAGGATCTGGCAGTGTGGAGGAACTTTGGAAATTGTTACATGCTCACATGTGGACATGTGTTTCGGG
AAGCCACACCTTACACATTTCCAGGAGGCACAGGCCAGATTATCAATAAAAATAACAAGACTACTTGCAGAAGTGTGGAT
GGATAAATTCAAAAATTTCTTCTATATAATTTCTCCAGGTGTTACAAAGGTAGATTATGGAGATATATCATCGAGACTTG
GTCTAAGGCACAAACTACATTGTAAACCTTTTTCTTGGTACCTAGAGAATATC

Alignment

ORF - retro_tsyr_1444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.87 %
• Parental protein coverage: 74.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRKFAYCKVVLATSLIWVLLDMFLLLYFSECNKCDEK-KERGLPAGDVLEPVQKPHEGPGEMGKPVVIPK
          MRKFAYCKVVLATSLIWVLLDMFLLLYFSECNKCDEK.KERGLPAGDVLEPVQK.H.GPGEMGKPVVIPK
Retrocopy MRKFAYCKVVLATSLIWVLLDMFLLLYFSECNKCDEK<KERGLPAGDVLEPVQKLHLGPGEMGKPVVIPK

Parental  EDQDKMKEMFKINQFNLMASEMIALNRSLPDVRLEGCKTKVYPDNLPTTSVVIVFHNEAWSTLLRTVHSV
          EDQDKMKEMFKINQFNLM.SEM.ALNRSL.DVRLEG.KTKV.PDNLPTTSVVIVFH.EAWSTLLR.VHSV
Retrocopy EDQDKMKEMFKINQFNLMVSEMTALNRSLQDVRLEGYKTKVHPDNLPTTSVVIVFHYEAWSTLLRNVHSV

Parental  INRSPRHMIEEIVLVDDASERDFLKRPLESYVKKLKVPVHVIRMEQRSGLIRARLKGAAVSKGQVITFLD
          INRSPR.MIEEIVLVDDASERDFLKRPLESYVKKLKVPVHVI.MEQ.SGLIRARLKG.AVSKGQVITFLD
Retrocopy INRSPRYMIEEIVLVDDASERDFLKRPLESYVKKLKVPVHVIQMEQCSGLIRARLKGVAVSKGQVITFLD

Parental  AHCECTVGWLEPLLARIKQD-RTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRK
          AHCECTVGWLEP.LARIKQD.RTVVCPIIDVIS.DTFEYMAGSDMTYGGFNWK.NF.WYPVPQREMDRRK
Retrocopy AHCECTVGWLEPHLARIKQDRRTVVCPIIDVISNDTFEYMAGSDMTYGGFNWKPNFHWYPVPQREMDRRK

Parental  GDRTLPVRTPTMAGGLFSIDRDYFQEIGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHV-GHVFRK
          GD..LP.RTPTMAGGLFSIDR.YFQEIGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHV.GHVFR.
Retrocopy GDWILPIRTPTMAGGLFSIDRGYFQEIGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHV<GHVFRE

Parental  ATPYTFPGGTGQIINKNN-RRLAEVWMDEFKNFFYIISPGVTKVDYGDISSRLGLRHKLQCNPFSWYLEN
          ATPYTFPGGTGQIINKNN.R.LAEVWMD.FKNFFYIISPGVTKVDYGDISSRLGLRHKL.C.PFSWYLEN
Retrocopy ATPYTFPGGTGQIINKNN>RLLAEVWMDKFKNFFYIISPGVTKVDYGDISSRLGLRHKLHCKPFSWYLEN

Parental  I
          I
Retrocopy I

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1444 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011206	1 retrocopy	retro_btau_581,
Callithrix jacchus	ENSCJAG00000021030	2 retrocopies	retro_cjac_1554, retro_cjac_865,
Myotis lucifugus	ENSMLUG00000001978	1 retrocopy	retro_mluc_163,
Mus musculus	ENSMUSG00000000420	1 retrocopy	retro_mmus_1312,
Ictidomys tridecemlineatus	ENSSTOG00000003311	1 retrocopy	retro_itri_954,
Tarsius syrichta	ENSTSYG00000004975	1 retrocopy	retro_tsyr_386,
Tarsius syrichta	ENSTSYG00000014610	1 retrocopy	retro_tsyr_1444 ,