RetrogeneDB ID: retro_tbel_3336

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_137712:60777..61511(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000017170
• Aliases: None
• Description: None

Sequence

>retro_tbel_3336
ATGGGAAAGGAGAAGACCATATAAATATCGTTGTCATTGGACACGTAGATTCAGGCAAGTCCATCACTACTGGTCATCTG
ATCTACAAATGCGGTGGAATTGACAAAAGAATCATCAAAAAAAAAAAAAATGAGAAAGAGGCTCTGAGATAGAAAAGGAC
TCCTCGAAGTATGCCTGGGTCTTGGATAAACTAAAAGCTGAATGTGAGCATGTTGTCACCATTAATATCTCCCTGTGGAA
ATTTGAGAACAGCAAATATTGTGTGACTGTCCTTGATGCCCCAAGACACAGAGACTTTATCAAAAACATGATTACAAGCA
CAACTCAAGCTGACCATGTTGTGCTGATTACTGTTGCTGGTGTTGGTAAATTTGAATCTGCTGTCTCCAAGAAGGAGAAG
ATCCATGAGCATGCCTTTCTGGCTTACTCACTGGGTGTGAAACAACTAATCCTTAGTGTTAACAAAATGGATTCTGCTGA
GCCATGCTACAGTCTAAAGATATGTGAGGAGATTCTTAAGTAAATCAGCACCTACATTAAGAAAATTGGTTACAATTCCA
ACACGCTATCATCGTGCCTGCTTCTGGTTGGAATAGTGACAACATGCTGAGCCAAGTGCCAACATGCCATGGTTCAAGAA
ATGGAAAGTCACTGTAAAGATGGCAATGCCAATGGAATTCTGTTCTAGATTGCATCCTACCATTAATCCTCTGGATTGCA
TACAACTAACAAGC

Alignment

ORF - retro_tbel_3336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.78 %
• Parental protein coverage: 68.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGKEKT-HTNIVVIEHVDSGKSTTSGHLIDKCGGVDQRIM--EKIEKEA-AEMGKGSFKDVWVLDKQKA-
          MGKEKT.H.NIVVI.HVDSGKS.T.GHLI.KCGG.D.RI......EKEA..E..K.S.K..WVLDK.KA.
Retrocopy MGKEKT<HINIVVIGHVDSGKSITTGHLIYKCGGIDKRIIXXXXXEKEA<SEIEKDSSKYAWVLDKLKAE

Parental  -EHGTTIGISLWKSETSKF-VTIIDG--HRDFIKNMITGT--ANCAVPIAAAAVGEPEAGIPKNGQTREH
          .EH..TI.ISLWK.E.SK..VT..D...HRDFIKNMIT.T..A...V.I..A.VG..E....K.....EH
Retrocopy CEHVVTINISLWKFENSKYCVTVLDAPRHRDFIKNMITSTTQADHVVLITVAGVGKFESAVSKKEKIHEH

Parental  ALLVYTLGVKQLMVGVNKMDSTESPYSQKRYKEIV--VSTYIKKVSTYNLDTV-VYVSISGWNGDNML-H
          A.L.Y.LGVKQL...VNKMDS.E..YS.K...EI....STYIKK...YN..T....V..SGWN.DNML..
Retrocopy AFLAYSLGVKQLILSVNKMDSAEPCYSLKICEEILK*ISTYIKKIG-YNSNTL<IIVPASGWNSDNML<E

Parental  PSANMPWFIGWKVTHKGGSANE--SKLHETLDRILALTYTT
          PSANMPWF..WKVT.K.....E..S.LH.T.........T.
Retrocopy PSANMPWFKKWKVTVKMAMPMEFCSRLHPTINPLDCIQLTS

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3336 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3336 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Tupaia belangeri	ENSTBEG00000012151	51 retrocopies	retro_tbel_1084, retro_tbel_1330, retro_tbel_1373, retro_tbel_1452, retro_tbel_166, retro_tbel_1841, retro_tbel_1969, retro_tbel_1994, retro_tbel_2088, retro_tbel_2091, retro_tbel_2179, retro_tbel_2205, retro_tbel_2206, retro_tbel_2218, retro_tbel_2232, retro_tbel_2419, retro_tbel_2505, retro_tbel_259, retro_tbel_2627, retro_tbel_2718, retro_tbel_2738, retro_tbel_2758, retro_tbel_282, retro_tbel_2976, retro_tbel_3032, retro_tbel_3065, retro_tbel_3067, retro_tbel_3281, retro_tbel_3307, retro_tbel_3315, retro_tbel_338, retro_tbel_354, retro_tbel_360, retro_tbel_372, retro_tbel_3813, retro_tbel_3865, retro_tbel_3967, retro_tbel_4125, retro_tbel_4192, retro_tbel_4282, retro_tbel_4352, retro_tbel_4370, retro_tbel_4466, retro_tbel_4496, retro_tbel_4639, retro_tbel_4660, retro_tbel_4695, retro_tbel_473, retro_tbel_588, retro_tbel_620, retro_tbel_903,
Tupaia belangeri	ENSTBEG00000017170	16 retrocopies	retro_tbel_1335, retro_tbel_1406, retro_tbel_2677, retro_tbel_2899, retro_tbel_2966, retro_tbel_3336 , retro_tbel_348, retro_tbel_3485, retro_tbel_3658, retro_tbel_3727, retro_tbel_3948, retro_tbel_4091, retro_tbel_4127, retro_tbel_4290, retro_tbel_4507, retro_tbel_4527,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,